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Normally these messages only flash for five minutes and then turn solid to indicate the system has started. However, if it keeps flashing, it could be due to a communication issue with the AC system. Air conditioning plays a crucial role in maintaining a comfortable indoor environment. Make sure to follow my troubleshooting steps below to get to the root of the problem.

honeywell thermostat flashing cool on

What Does the “Cool On” or “Heat On” Indicator Mean?

During normal operation, the “Cool On” or “Heat On” message stays lit depending on the temperature mode. So if the air conditioner is working to cool down the house, the thermostat will say “Cool On.” It is important to set the thermostat to ‘cool mode' to ensure proper cooling. Meanwhile, if the heat pump is working to heat up, the thermostat will instead display “Heat On.”

“Cool On” indicator on a Honeywell T6 display

T6 Pro Smart Cool On Flashing
“Cool On” indicator on a Honeywell T6 display

Compressor Protection Feature

However, if either of these messages are flashing it can imply that the thermostat is running the compressor protection feature, known as the delay mode. The delay mode helps protect the compressor by preventing wear and potential damage.

In some models, this message is displayed as “Waiting for equipment”. The thermostat activates a startup delay to protect the compressor from voltage fluctuations after a power loss, allowing the AC system to reset and readjust to normal operating conditions.

As the name suggests, it’s an intentional safety feature to prevent any harm to your compressor, especially in the event of a power outage.

By taking about 5 minutes to cycle, the thermostat ensures that everything runs smoothly and avoids the damage caused by intermittent power cuts or surges.

So after you’ve just recovered from a power cut, the “Cool On” or “Heat On” message would stay flashing for five minutes. After which, it will remain solid and the HVAC system will kick in.

10 Steps to Troubleshoot a Honeywell Thermostat Flashing Cool On or Heat On Indicator

When the “Cool On” or “Heat On” indicator continues to flash for more than five minutes without hot/cold air coming in, it can indicate a malfunctioning thermostat. If the issue persists, it is important to consult an HVAC professional to diagnose and resolve the problem.

If so, I recommend following the troubleshooting steps laid out below.

1. Wait 5-10 minutes

Your thermostat could be facing a slight delay in restarting and activating its compressor protection feature, which is often indicated on the thermostat display.

Make sure to wait at least 5 minutes before further troubleshooting. I recommend waiting for a solid 10 minutes so you can confidently rule out the compressor protection feature.

Room Temperature Not Reaching Thermostat Setting

2. Set the Thermostat to its Lowest Temperature Setting

You can verify the thermostat’s ability to manage the cooling system by adjusting its settings.

  • First, set the thermostat to the lowest possible temperature.
  • Ensure that the mode is set to “Cool” and that the fan setting is on “Auto.”
  • After making these adjustments, give it some time.
  • Check if the AC comes to life or if you experience any change in the room’s temperature, specifically if cool air is being emitted from the vents.

This will help determine if the thermostat is effectively controlling the temperature function.

3: Check if the Thermostat is in Setup Mode or if the Clock is Set

In certain models, when the thermostat is recovering from a power outage, it may revert to setup mode, causing the “Honeywell thermostat cool on” lights to blink.

To resolve this, check your thermostat’s settings and make any necessary adjustments.

Also, verify that the time displayed on your thermostat is accurate. An incorrect time setting can interfere with the schedule settings and glitch out the thermostat.

alkaline batteries

4: Check the Thermostat Batteries/Power Connection

Weak batteries can prevent your thermostat from initiating the cooling process.

To fix this, replace the thermostat batteries by removing the thermostat from the wall mount and replacing the batteries on the back of the panel.

T6 Battery Replace
Batteries located at the back of the thermostat panel

If your thermostat uses a 24 VAC power source instead of batteries, inspect the wiring.

To do so:

  • First, turn off the power to your HVAC system.
  • Next, remove the thermostat, ensuring you unscrew it first if necessary.
  • Then, examine the C-wire to confirm its proper connection.
  • Make sure there is no dust, dirt, or debris, and clean the contacts.
  • You can also try reconnecting the terminals, making sure they are secure.
  • Additionally, check the circuit breaker to ensure it hasn't tripped, as this can affect the power supply to your thermostat.

Check out our guide on how to change Honeywell thermostat batteries

5. Check the Voltage at the Thermostat Contacts

If you know how to troubleshoot electrical components and you already have a multimeter, you can check the voltage in the thermostat wires. 

Make sure that the R and C contacts have a voltage between 24-30V; lower values might indicate insufficient power.

6. Check the Power in Each Component of the Cooling System

If the previous steps haven’t resolved the issue, you’ll need to diagnose the rest of the HVAC system.

  • First, inspect the power supply of your air handler, fans, furnace, AC unit, and outdoor unit.
  • Watch out for unusual humming or clicking noises coming from your equipment, as these might indicate a problem.
  • Also, examine the power supply for each device.
  • Make sure that connectors and sockets are appropriately plugged in, and switches are turned on.
  • While examining your equipment, check if the doors or panels are properly closed. Loose or detached parts and any obstructions may cause the safety switches to disconnect, especially the furnace door.
  • If possible, check the fuses or switches visually or by using the continuity setting on a multimeter
  • Then, inspect your circuit breakers for any irregularities.
  • Try turning your equipment on and off, as well as resetting the breaker corresponding to these devices.

7. Check the Indoor AC Air Filters

It’s essential to regularly inspect your indoor AC air filter to make sure it doesn’t need replacing. Replacing air filters every three months is crucial for maintaining optimal performance.

A clogged or dirty filter hinders proper airflow and can lead to decreased cooling efficiency and poor air quality inside your house.

It can also put extra strain on your thermostat and other equipment, ultimately leading to higher energy bills.

So I recommend making it a habit to change your AC filter every three months or as recommended by the manufacturer.

Heat Pump

8. Check AC Coils and See if they are Dirty

The external AC coils can also become dirty or blocked over time.

  • As the coil accumulates dirt, it hampers proper airflow and reduces its ability to absorb heat and adequately cool the air.
  • Inspect your AC unit's coils to see if there is buildup on the fins, indicating the need for a thorough cleaning.
  • However, always make sure the unit is turned off before attempting any cleaning or maintenance.
  • To reduce the chances of clogging and improve efficiency, keep the area around the AC clean and provide ample space for airflow by removing any nearby plants or debris.

9. Reset your Thermostat

In some cases, resetting your thermostat to factory defaults might be necessary.

Keep in mind that this process will erase your settings and programmed schedule, so it's a good idea to take note of any configurations you don't want to forget.To reset a Honeywell thermostat, check out my detailed reset guide which covers all Honeywell thermostat models.

Thermostat Wire Colors

10. Bypass the Thermostat

If you’re somewhat more skilled at DIY, especially when it comes to dealing with electrical components, you can try to bypass the thermostat. 

However, make sure you have a multimeter and a proper tool to create a jumper wire.

  • First, turn off the power switch on the furnace or air handler, and also disconnect the thermostat from the breaker.
  • Then, take out the thermostat from the wall mount.
  • After that, run one end of a jumper to R (Power) and the other end to Y (Cooling) or W (Heating) on the thermostat contacts.
  • With this setup in place, turn the power back on and check if the AC or furnace/air handler turns on. 
  • If these components turn on without any issue, the thermostat is indeed defective.

Final Step: Call in the Professionals!

When you’ve exhausted all possible solutions and your thermostat is still flashing “Cool On,” it’s time to get the help of an HVAC technician.

  • A trained technician can likely pinpoint the problem and fix it with ease.
  • Some common issues that may require professional intervention include damaged wiring, a malfunctioning capacitor, an obstructed sensor, or a blown fuse.
  • In addition, components like the compressor, condenser, or fan motor may need further inspection.
  • For a recently installed thermostat, an expert can verify proper wire connections and ensure the device is set up correctly for your specific HVAC system.


If the Cool On or Heat On message is flashing for more than five minutes, it will require you to troubleshoot the entire HVAC and air conditioning system.

The troubleshooting guide above will help you do just that so if you follow those steps, you’ll be able to get to the root cause in no time.

However, if you aren’t able to check the circuit breakers or the rest of your HVAC system, always get a professional to help you.


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