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In case you notice that your Honeywell thermostat is persistently making clicking noises which adversely affect your heating or cooling system's performance, fret not. You are in the right place.

Most of the time, this issue is due to batteries that are on the way out, or loose wiring from the HVAC system to the thermostat.

So keep reading and I’ll show you how to troubleshoot the issue, step-by-step.  

At SmartHomePerfected we always advise readers not to undertake any work they are not competent in performing and if in any doubt, it is best to seek the assistance of a professional.

What is the Clicking Sound in Thermostats?

A thermostat clicking sound is actually quite normal, as it signifies the activation of a relay that sends a signal to either the heating or cooling system, depending on your settings or schedule.

When your thermostat's display is powered on, responds to your commands, and emits the familiar clicking sound, it's usually an indication that the issue may be within the wiring or HVAC components rather than the thermostat itself.

However, it's still possible that the thermostat could be malfunctioning. So in the steps that follow, I’ll start by troubleshooting the thermostat to ensure it's operating correctly before moving on to the rest of the system.

Step 1: Wait 5-10 minutes

When a Honeywell thermostat clicks but nothing happens, your first action should be to wait 5-10 minutes.

This is because of the compressor protection feature which prevents your HVAC system from turning on too quickly after events like power cycling, power outages, flipped switches or tripped breakers, or even after changing your thermostat's batteries.

During this time, you may notice messages on the thermostat display such as flashing “Cool On,” “Heat On,” “Wait,” or “Waiting for equipment.”

By waiting more than 5 minutes, you can safely rule out the possibility of the compressor protection feature causing the issue.

However, if the system clicks, and the flashing messages disappear, but your system still hasn't turned on, then it's time to move on to the next step.

Step 2: Replace the Batteries on the Thermostat

Another reason your Honeywell thermostat may click without initiating a response could be due to weak batteries.

If it has been a while since you last changed the batteries in your thermostat, it's time to put in a fresh set.

  • To replace the batteries, carefully remove the thermostat cover and locate the battery compartment.
  • Swap out the old batteries with new, high-quality replacements, ensuring proper placement of the positive and negative ends.
  • Once you've successfully installed the new batteries, replace the thermostat cover and test the device.

A simple battery change might just resolve the issue, restoring your thermostat's performance.

Replace batteries
How to replace the batteries on most Honeywell thermostat models

Step 3: Check for Loose Wiring

If a battery swap didn’t fix the issue or your thermostat doesn’t run on batteries, you can then start checking the thermostat wires and connections. 

  1. Begin by carefully removing the thermostat from its wall mount panel.
  2. Inspect the area for any loose wires that may be causing the issue, you can gently tug on each wire to tell if they are loose
  3. If you have already turned off the power and feel confident in handling electrical components, consider taking out the wires, giving the contacts a thorough cleaning to remove dust, and reinstalling them.
  4. Ensure that all connections are secure, and the thermostat wires are correctly positioned you can gently tug on them again to see if they are secure.
  5. Additionally, if you can safely access the thermostat wiring strip near the furnace, or check the entire length of the wire running from the thermostat to the control board, examine for damaged wires, weak splices and wrong connections

This thorough inspection should help you identify any potential wiring issues that may be preventing your Honeywell thermostat from functioning properly. You don’t always have to do this yourself, so try to get help from a professional. 

Step 4: Try Bypassing the Thermostat

To figure out if the thermostat is to blame, you can try bypassing it.

  1. First, remove the thermostat from its wall mount.
  2. Then, using a jumper wire, connect one end to the R terminal and the other end to either the Y terminal (for cooling) or the W terminal (for heating).
  3. Finally, turn the power back on.
  4. If the AC or heating kicks in without any issues after bypassing the thermostat, you can confirm that the thermostat is the source of the problem.
  5. For good measure, try testing both W and Y to confirm if both the heating and cooling systems are operational.
  6. However, don't forget to switch off the power whenever you're working on the wire connections

On the other hand, if the heating or cooling still fails to activate, the issue is likely within the rest of the HVAC system.

Step 5: Check the Breakers On Your HVAC System

Take a moment to inspect the breakers or safety switches assigned to your HVAC system.

In some instances, you may have separate breakers for each part. If you discover any that have tripped, simply reset them and see if the problem resolves itself.

Keep in mind that after resetting the breakers, your thermostat could potentially take another five minutes or more to recognize that the other components are powered up and functioning properly.

So be patient and give the thermostat time for the entire HVAC system to start working as usual.

Breakers generally trip for a reason, so you'll need to consult a technician to figure out whats causing them to trip.

Step 6: Check Air Filters and Replace them as Necessary

When the filter is dirty, it restricts airflow, making it difficult for the unit to function correctly. So with limited airflow, the safety switches within the HVAC system won’t allow the heating or cooling systems to turn on.

Therefore, it’s a good idea to inspect the filters and see if they are covered in dust and debris. If so, it's best to clean or replace them.

After taking these measures, reinsert the filters and attempt to turn the system on. Also, take this opportunity to examine the AC coils.

If they are clogged up, you might have to clean it yourself or get help from a duct-cleaning service.

HVAC Filter
Replacing your air filters regularly will help maintain the HVAC system from tripping out

Final Step: Call in a professional

After attempting all the above troubleshooting steps for your Honeywell thermostat, it's crucial to know when to stop as going beyond this step can potentially lead to more harm than good.

Instead, it’s best to rely on the knowledge and skills of an expert to tackle the issue.

A trained and certified technician can efficiently analyze the situation and identify the root cause of the clicking without carrying out any significant changes in your system.


A Honeywell thermostat that clicks but won’t power on the heating or cooling system usually indicates an issue with the wiring and the rest of the HVAC components.

Checking the wiring or if individual HVAC components can power up will help you get to the root of the problem sooner.

However, I recommend getting the help of a professional if the issue goes beyond a simple battery replacement or wiring check.


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