I have the exact same problem- Federal tax withheld from an ESA and Form 1042-S issued instead of 1099-Q even though I'm a US citizen.

I used all of the distribution on qualified expenses. In your answer, why did you advise to file a 1099-Q form only if the distribution was used for unqualified expenses? I'm worried if I don't file a 1099-Q that the IRS won't know to what the "Other taxes withheld" pertain. Note that I don't qualify for an education credit as my income is too high.

Thanks!

Here is the best way to report and then exclude the income since it is for qualified educational expenses.

To report the 1042-S 

1. Open your return in TurboTax 
2. Click on Wages & Income 
3. Scroll down to All Income
4. Scroll down to Less Common Income 
5. Scroll down to Miscellaneous Income, 1099-A, 1099-C 
6. Click start 
7. Scroll down to Other reportable income 
8. Answer yes and record this as 1042S income and then the amount.

Now to exclude it since these are used as qualified educational expenses

1. Repeat steps 1-7.
2. Record this as a 1042S Distribution for qualified Educational Expenses. 
3. Now enter the amount with the minus sign in front of the income
4. You have now reported the 1042S and then excluded the income.

To report the US tax paid:

1. With your return open
2. Click on Deductions & Credits
3. Scroll down to Estimates and Other Taxes Paid\
4. Click on Other Income Taxes
5. Scroll down Other Income Taxes
6. Click on Withholding not already entered on a W-2 or 1099

@yorgo 

I followed these instructions and for some reason adding the income under Other Misc Income and then adding a line with the same income as a negative number increased my Federal Refund (by $241) even though the Total Misc Taxable Income is listed as $0. Why is this - it seems like this shouldn't affect the Federal Refund?

Yes, this does seem unusual. To look at this in detail, we would like to see a diagnostic copy of your return. The information in this file is a sanitized copy meaning there is no personal information, only numbers so that we can troubleshoot in depth, check for calculation issues, and to see how certain items are applied. Here is how to order. 

For Turbo Tax online, go to tax tools>tools>share my file with agent.  When this is selected, you will receive a token number.  Respond back in this thread and tell us what that token number is. 

If you use the desktop version, go to the black stripe at the top of the program>online>send tax file to agent. Once you receive the token number, reply back in this thread and let us know what that token number is.

@yorgo 

I have shared a protected copy of my return online. My token number is 1203288. 

Thank you for offering to help further with this - much appreciated!

I have reviewed your file and noticed a $115 difference rather than a $241. The increase was due to a difference in the foreign tax credit that you can claim this year thus reducing the carryover into next year. It's a calculation that is determined in the Foreign Tax Worksheet that involves a series of ratios in changes between foreign versus total income.

I can report this discrepancy to our developers to see if this is a calculation issue.  However, this has minimal impact in your tax return thus I suggest you can safely file this return without negative consequences. 

@yorgo 

I have listed the Form 1042-S income and qualified Education Expenses as you suggested and I have submitted my tax return.

Thank you very much for your expert help- I very much appreciate it.