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IRS.gov Website
Publication 15-A
taxmap/pubs/p15a-002.htm#en_us_publink1000169523

3. Employees of Exempt Organizations(p9)

rule
Many nonprofit organizations are exempt from federal income tax. Although they do not have to pay federal income tax themselves, they must still withhold federal income tax from the pay of their employees. However, there are special social security, Medicare, and federal unemployment (FUTA) tax rules that apply to the wages that they pay their employees.
taxmap/pubs/p15a-002.htm#en_us_publink1000169524

Section 501(c)(3) organizations.(p9)

rule
Nonprofit organizations that are exempt from federal income tax under section 501(c)(3) of the Internal Revenue Code include any community chest, fund, or foundation organized and operated exclusively for religious, charitable, scientific, testing for public safety, literary or educational purposes, fostering national or international amateur sports competition, or for the prevention of cruelty to children or animals. These organizations are usually corporations and are exempt from federal income tax under section 501(a).
taxmap/pubs/p15a-002.htm#en_us_publink1000169525
Social security and Medicare taxes.(p9)
Wages paid to employees of section 501(c)(3) organizations are subject to social security and Medicare taxes unless one of the following situations applies.
An employee of a church or church-controlled organization that is exempt from social security and Medicare taxes must pay self-employment tax if the employee is paid $108.28 or more in a year. However, an employee who is a member of a qualified religious sect can apply for an exemption from the self-employment tax by filing Form 4029, Application for Exemption From Social Security and Medicare Taxes and Waiver of Benefits. See Members of recognized religious sects opposed to insurance in section 4 on page 10.
taxmap/pubs/p15a-002.htm#en_us_publink1000169526
Federal unemployment tax.(p10)
An organization that is exempt from federal income tax under section 501(c)(3) of the Internal Revenue Code is also exempt from FUTA tax. This exemption cannot be waived. Do not file Form 940 to report wages paid by these organizations or pay the tax.
Note.An organization wholly owned by a state or its political subdivision should contact the appropriate state official for information about reporting and getting social security and Medicare coverage for its employees.
taxmap/pubs/p15a-002.htm#en_us_publink1000169528

Other than section 501(c)(3) organizations.(p10)

rule
Nonprofit organizations that are not section 501(c)(3) organizations may also be exempt from federal income tax under section 501(a) or section 521. However, these organizations are not exempt from withholding federal income, social security, or Medicare tax from their employees' pay, or from paying FUTA tax. Two special rules for social security, Medicare, and FUTA taxes apply.
  1. If an employee is paid less than $100 during a calendar year, his or her wages are not subject to social security and Medicare taxes.
  2. If an employee is paid less than $50 in a calendar quarter, his or her wages are not subject to FUTA tax for the quarter.
The above rules do not apply to employees who work for pension plans and other similar organizations described in section 401(a).