Setting up a checking account for a nonprofit organization isn't difficult provided you already have official status as a non-profit. However, often the filing of articles of incorporation and establishing a checking account are done at about the same time. You need to take each step in order not to run afoul of tax laws.
Establishing nNonprofit Status
File articles of incorporation for nonprofit organizations in the state where the organization operates. The articles consist of a form that may be available online that identifies the organization and its purpose, incorporators or directors, and the organization's mailing address. The incorporators must sign the form, and there is usually a fee for filing.
Fill out Form SS-4 with the U.S. Internal Revenue Service to obtain an Employer Identification Number (EIN). This is the same form used by all businesses, so check the box that identifies the group as a church or church-controlled organization, or as an "other nonprofit organization." For the later, specify the type of organization, such as an educational organization.
Enter your reason for applying for an EIN on Line 10 of form SS-4, listed in a series of check boxes including for "Banking purposes only" if the organization has no employees.
Take your EIN once you received the federal number to the bank and fill out the institution's application for a checking account. Each bank will have it's own forms and procedures, but many offer free checking to non-profits.