Late filers can be penalized $100 per day until their returns are filed. Note that if you are a board member of a nonprofit that files late, in some states such as California you can be held personally liable for the late filing penalties! A nonprofit that fails to file Form 990, 990-EZ or 990-N three years in a row will have its tax-exemption automatically revoked.
Apply for Form 990 Extension
Extensions can be filed online at http://efile.form990.org/. A fillable version of the form can be downloaded from the IRS website.
Remember that Form 990 and extensions for calendar year organizations must be filed or postmarked by Friday May 15. If a hardcopy is submitted, be sure to use certified mail or FedEx or UPS overnight or 2nd day air. Your receipt is the only proof acceptable to the IRS that the organization filed its return or extension on a timely basis.