Late file Federal refund due/Penalty on Estimated Tax?

Yes, even if you file an extension you can apply your 2023 refund to 2024 taxes.  

As you said the IRS already has the money, You just have to authorize them to do it.

 

To do this, log into your account.

 

            

 

1. Select Tax Tools
2. On the drop-down select Tools
3. There will be 4 green boxes
4. Select Topics Search
5. Type Apply refund to 2024 tax return
6. The screen Get Your Refund Now or Apply It to Next Year's Taxes will appear
7. Select to apply the refund to 2024.

                

Although you wont file until later in the year.  The IRS has had the money since before April 18th, so it can be applied to your first quarter payment.

 

@JohnB5677 

 

My question remains unanswered--

 

will the IRS apply an underpayment of estimated taxes penalty in this case?

I'm sorry,  I wasn't clear.

 

No, you will not get an underpayment penalty for estimated taxes, provided you make all the payments for the proper amount due and timely.

1. If your refund will exceed your first quarter payment, you can apply it as the first payment.
2. If your refund is less than the required first payment, you must make up the difference.
3. If your refund is grater than the required first payment, you can take the excess portion and apply it to the second quarter, and so on.

As stated above:

"The IRS has had the money since before April 18th, so it can be applied to your first quarter payment."