The IRS on its website notes:

Electronic filing is quick, secure, and more accurate than filing a paper return; and e-filing provides fast acknowledgment that the IRS has received the return.  E-filing reduces normal processing time and makes compliance with reporting and disclosure requirements easier.  Charities and non-profits can file the following forms electronically through an Approved IRS 990-efile Provider.

  • Form 990
  • Form 990-EZ
  • Form 990-PF
  • Form 8868 (Application for Extension of Time to File an EO Return)
  • Form 1120-POL
  • Form 7704 (extension form for the 1120-POL)

One such Approved Provider is The Urban Institute, which offers a a web application called NCCS 990 Online.  The service is FREE for organizations with less than $100,000 in gross receipts.

E-filing of Form 990 and 990-PF is required for certain large tax-exempt organizations.  For tax years ending after December 31, 2006, this requirement applies to exempt organizations with at least $10 million in total assets if the organization files at least 250 returns (including W-2s) in a calendar year.  Private foundations and non-exempt charitable trusts must file Form 990-PF electronically regardless of their asset size if they file at least 250 returns annually.

Read more here.