Help! My Puppy Hates Its Crate: What Can I Do?

Is Your Puppy Crying All Night in the Crate or When You Leave the Room? Here’s What to Do

If you’ve just brought home a new puppy, you’ve probably heard that crate training is one of the most effective ways to housebreak them and prevent unwanted behaviors when you can’t supervise.

But what if your puppy cries all night in the crate or screams for hours when you leave it alone?

When a puppy shows ongoing signs of distress in a crate or when separated from you, it may be more than just an adjustment issue. These behaviors can signal early signs of puppy separation anxiety.

Much like a panic attack in humans, separation anxiety can cause your puppy to spiral into stress when confined or left alone, making it hard for them to settle or self-soothe.

In this article, we’ll break down the common signs of puppy separation anxiety, what causes it, and the first steps you can take to help your pup feel safe, calm, and confident when they’re on their own.

Why Does My Puppy Cry for Hours in Its Crate?

A puppy may whine or cry in their crate for many reasons, including:

• Boredom: Puppies may cry to get attention or because they have nothing to do. Puppies are naturally energetic and need mental stimulation.

• Needs to go outside: Puppies may cry if they need to urinate or defecate. Since puppies have small bladders, they may need frequent potty breaks, especially during the night.

• Negative associations: Puppies may have developed negative feelings about the crate if they were crated for too long, left to “cry it out,” or confined with too many other puppies, making the crate feel like a stressful or unsafe place.

• Transitional anxiety: Puppies may cry because they are lonely and miss their mother and littermates. This is common as they adjust to their new home.

However, if your puppy cries for 30 minutes or more after being confined in a crate or playpen, or if they react similarly when left alone in any space, they are most likely experiencing separation anxiety.

Early Signs of Puppy Separation Anxiety 

An example of the distress calls and escape attempts of a puppy with separation anxiety.

Puppies naturally seek comfort and security, especially from their human family, whom they see as their “pack.”

However, when confined in a crate or playpen (or left alone), they might feel isolated and anxious. This can lead to distress vocalizations such as nonstop whining, crying, barking, or howling, as well as frantic escape attempts that could cause harm to your puppy, all of which are early signs of separation anxiety in dogs.

The key is understanding that these behaviors aren't acts of defiance but are usually driven by stress and anxiety.

The key indicators of separation anxiety include:

• Anxious body language: A furrowed brow, pinned-back ears, a tucked tail, and wide “whale eyes” (where you see the whites of their eyes) are clear signs of stress.

• Loss of bladder or bowel control: An anxious puppy may urinate or defecate in their crate or playpen, or when left alone.

• Distress vocalizations: Some puppies may escalate to high-pitched, frantic vocalizations—screaming or crying for hours in the crate—which can be deeply distressing for the puppy and concerning (or frustrating) for anyone within earshot.

• Excessive panting, pacing, or drooling: Puppies under stress may pant heavily, pace nonstop, or become soaked in their own drool.

• Destructive behaviors: Biting on the crate bars, chewing through the crate liner, and digging frantically as if attempting to escape the crate can occur if your puppy is in distress. They may also destroy anything nearby, like furniture or your belongings, out of frustration.

These symptoms generally appear immediately or within the first few minutes of being confined or left alone, and if left unresolved, may persist for hours until the puppy is freed or reunited with you.

Understanding the Root Cause of Puppy Separation Anxiety

Puppies are naturally pack animals, relying on their pack for safety and survival. When separated from you, they can feel vulnerable and insecure, which activates their instinct to stay close to the pack.

At the heart of separation anxiety in puppies lies their natural pack instinct. Dogs are hardwired to stay close to their family, so it's no surprise your puppy wants to follow you from room to room. This instinct helps them feel safe and connected.

But, when they’re suddenly left alone or confined in a crate or playpen where they can’t see or follow you, it can trigger panic. To them, being separated goes against everything their instincts tell them is safe.

Common situations that can provoke puppy separation anxiety include:

• First time being separated from litter: Puppies separated from their dam and littermates for the first time may struggle with separation anxiety.

• Sudden changes: Moving to a new home, changes in routine, or periods of isolation can trigger feelings of insecurity.

• Over-attachment: Puppies accustomed to constant attention and physical closeness may struggle to cope with being alone.

Understanding your puppy’s natural urge to stay close to their pack—and helping them learn to relax when those instincts are triggered—is key to building their confidence and sense of security when separated from you. That’s why gentle, positive crate training plays such an important role in their emotional development.

How Puppy Separation Anxiety Can Impact Your Life

A puppy that cries, barks, and howls for hours in their crate can leave you sleep-deprived, strain relationships with neighbors, and add stress to your workday, especially if you're working from home.

In an effort to avoid the chaos, you might be tempted to stop confining your puppy altogether. But without gradually teaching them how to feel safe alone, you risk raising an adult dog who panics whenever they’re separated from you—making everyday independence a long-term struggle.

Many puppy parents also experience guilt about leaving their dog alone, which can lead to tough (and costly) decisions, like bringing your pup everywhere you go or relying on doggy daycare or pet sitters.

That guilt, while understandable, can make it even harder to navigate your puppy’s separation anxiety. Balancing your puppy’s emotional needs with your own routine and responsibilities is challenging—but with the right approach, it’s absolutely possible.

Where to Put Your Puppy’s Crate to Prevent Separation Anxiety

Nightime Crate Placement

When it comes to crate training your puppy, choosing the right location for their crate is crucial for their comfort and your peace of mind. The best place to put the crate overnight is in your bedroom near the head of the bed. Here’s why this setup works effectively for both you and your puppy:

1. Proximity for Potty Breaks

Placing the crate in your bedroom allows you to hear your puppy if they need a potty break during the night. Puppies have small bladders and may need to go out several times, especially during their early months. Being nearby ensures you can respond promptly to their needs.

2. Providing Comfort and Security

Newly separated from their mother and littermates, puppies are not accustomed to being alone. Puppies are babies; they need to feel safe. Having their crate next to your bed can provide that sense of security. If your puppy wakes up, your presence will help calm them down.

3. Easy Reassurance

If your puppy cries and you’re confident it’s not for a bathroom break (for instance, if they’ve just been out or have access to pee pads), you can easily reach down and place your hand on the door of the crate to comfort them. This reassurance can help soothe their anxiety without necessarily letting them out of the crate, reinforcing that it is a safe space.

4. Gradual Transition

If your ultimate goal is for your puppy to sleep in a different location, you can gradually move the crate to that area once they are house-trained and more comfortable being alone. This transition can help them adapt to their new sleeping arrangement while still feeling secure.

Daytime Crate Placement

During the day, try placing your puppy’s crate or playpen in a common area where you spend time, like the living room or home office. This allows your puppy to enjoy crate time or safely play in a pen while still being near you. Staying close to “the pack” helps your puppy feel more secure and builds positive associations with confinement.

How to Train a Crying Puppy to Settle Down in a Crate

Watch a Bernedoodle puppy with separation anxiety learn to relax in his crate through gentle, specialized training designed to build comfort and confidence.

While separation anxiety is common in puppies, the good news is that they can learn to feel comfortable being confined or left alone—with the right approach.

At Dog Savvy, we’ve developed a gentle and effective method called Doggie Decompression Training to help puppies settle and relax when confined to a crate or playpen.

Here’s how to get started:

1. Stay Nearby Until Your Puppy Settles

It’s a common myth that letting a puppy "cry it out" will help them adjust. In reality, leaving an anxious puppy alone can heighten their distress. Instead, stay nearby and within your puppy’s line of sight. Your calm presence reassures them that they’re not abandoned, even if you're not actively engaging.

2. Ignore the Crying—Without Leaving

While staying nearby, it’s important not to reinforce whining or barking with your attention. That means no talking, eye contact, or petting. Simply be present and wait for your puppy to settle. This helps them learn that calm behavior is what earns your attention and freedom—not fussing.

3. Give Breaks After Calm Behavior

Once your puppy has settled in the crate, reward them with a short break. Take them outside to potty, let them stretch, or offer a quick drink of water—but keep everything low-key. The goal is to reinforce calm behavior without overstimulating them.

4. Use Treats to Build Positive Associations

Make the crate a rewarding place to be. Toss a handful of treats inside every time your puppy re-enters the crate. You can also feed meals or offer a long-lasting chew (like a bully stick) or an enrichment toy (like a stuffed Kong) inside the crate to help your puppy associate it with safety, comfort, and good things.

5. Repeat and Gradually Increase Time

Practice this process several times per session, slowly extending how long your puppy spends in the crate. Over time, your puppy will learn that the crate is a calm, secure space—and that being confined or alone doesn’t mean being abandoned.

Troubleshooting Crate Training

If your puppy is struggling to calm down in a crate, here are some additional tips:

• Try a playpen: During the day, a playpen gives your puppy more space to move around, which may help reduce anxiety.

• Use a soft crate: At nighttime, a soft carry crate can be put on a bed so that a puppy can feel close to you but still be contained.

• Soothing strategies: Place a familiar object—like a t-shirt that smells like you—inside the crate to help comfort your puppy. You can also sit nearby and gently rest your hand on the side of the crate or playpen, allowing your puppy to sniff and touch your fingers. This small connection can be incredibly calming and reassuring as they settle.

Common Crate Training Mistakes to Avoid

• Using the crate as punishment: The crate should always be a positive space. Never use it to discipline your puppy.

• Expecting too much too soon: Some puppies need more time to adjust. Pushing too hard can make anxiety worse.

• Not addressing the root cause: If anxiety persists, it’s essential to seek help from a professional to ensure you’re addressing the problem effectively.

In Conclusion, Be Patient and Consistent

By placing your puppy’s crate in your bedroom at night and somewhere they can see you during the day, you’re not only ensuring their comfort and security but also facilitating successful potty training and crate acclimation.

Ensuring good things happen in the crate, such as being fed a meal or getting lots of treats, can help a puppy learn to like their crate.

Crate training and overcoming separation anxiety take time, and each puppy is different. Most puppies will start to show improvement within a few weeks of consistent training. However, some may take up to six weeks or more to fully adjust to being alone in a crate.

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Need Help Training Your Puppy to Settle Down in Their?

If your puppy is still struggling no matter what you do, don't hesitate to reach out for professional guidance.

At Dog Savvy, we specialize in treating puppy separation anxiety and helping anxious puppies settle into their new homes. Our 6-week Puppy Separation Anxiety Training program is designed to help both you and your puppy succeed.

Click the link below to book an intro session with our puppy separation anxiety trainer and start seeing improvements today!

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About the Author

Alexandra Bassett is the lead dog trainer and behavior consultant at Dog Savvy, a private dog and puppy training company specializing in game-based dog training and behavior training solutions for dog separation anxiety, leash reactivity, excessive barking, and aggression.

She is certified as Knowledge Assessed by the Council of Professional Dog Trainers (CPDT-KA) and is available for online dog training sessions via Zoom.