Questions about changing fiscal years with the IRS have come up several times in the last few months, this one is the most recent:
I work with a non-for-profit that uses a calendar year to file 990 but a fiscal year for budgeting. As the organization grows, we think it would be simpler to have them both the same, but a calendar year end is problematic so we want to switch our IRS filing year end. What do we need to do to make this switch?
You will have to do a short year 990 filing as well as submitting a form 1128 to the IRS (the form instructions are here), the details can be found here. You should have available your tax exempt ruling letter from the IRS as you will need to submit a copy along with the form. If your nonprofit has only had to file a 990N with the IRS, you may not have to file the 1128 form. Please read the instructions to form 1128 for more details
For the short year filing, if you need to get an extension to file your 990, you’ll have to file one by the initial due date for your new fiscal year.
You should also look over any of your organizing documents to see if they contain any mention of your current fiscal year. You may need to amend those and refile them with the relevant state agencies and the IRS.