Nonprofits in San Francisco, California

San Francisco, California has a substantial nonprofit footprint on NonprofitTruth, with 29 organizations whose IRS Form 990 lists this city as the principal office. Combined revenue from San Francisco-headquartered nonprofits exceeds $10 billion, putting it in the top tier of U.S. nonprofit cities. The largest single category by revenue is Health.

San Francisco, California is home to 29 of the nonprofits we track. City pages aggregate organizations whose IRS Form 990 lists this city as the principal office — local affiliates of national networks may also operate here without appearing in this list.

The 29 San Francisco nonprofits in this view together report $17.3B in combined annual revenue on their most recent IRS Form 990 filings. Median revenue is $71.1M, and the simple average is $596.2M — a gap that reflects the long-tail distribution typical of the nonprofit sector, where a handful of large organizations account for most aggregate dollars.

Across the 29 San Francisco nonprofits we track, 2 earn an A and 10 earn a B on the Efficiency Score (combined 41% in the top two tiers, with A-grade organizations alone at 7%). Another 8 land at C, 7 at D, and 2 at F — a combined 31% in the bottom two tiers based on financial reserves, revenue-growth consistency, and officer-comp ratio drawn from each organization's most recent Form 990.

Across the San Francisco nonprofits where Schedule J compensation is reported, the average top executive received $4.8M in total compensation in the most recent filing year. The 990's Part VII and Schedule J break out base pay, bonuses, deferred compensation, retirement plan contributions, and non-taxable benefits separately.

City-level pages aggregate organizations whose principal office is in San Francisco. That includes locally founded charities, regional affiliates that file independently, and national organizations whose headquarters happen to sit here. Reading any one organization’s 990 starts with Part I (summary), then Part VIII (revenue), Part IX (functional expenses, where the program ratio comes from), and Part VII / Schedule J (compensation).

The NonprofitTruth Efficiency Score is a 0–100 composite that summarizes three signals the IRS Form 990 feed actually reports: financial health and months of operating reserves on the balance sheet (40% of the score), revenue-growth consistency over multiple years (35%), and current-officer compensation as a share of revenue (25%). It does not include a program-spending ratio — total program service expenses are not exposed by the ProPublica Nonprofit Explorer feed, and we do not estimate that figure. The grade A–F mapping is purely descriptive — it summarizes the financial structure that the 990 reveals, not the social impact, program quality, or outcomes of the work the organization does. Donors evaluating impact should pair these financial signals with program-level evaluations from sources like Charity Navigator, GiveWell, or the organization's own audited reports.

Many smaller San Francisco organizations file the abbreviated Form 990-EZ. The EZ form does not require the same level of compensation detail as the full 990, so the CEO-pay column may be blank for some entries even when the organization has paid leadership.

All financials on this page come from each organization's IRS Form 990 — the federal information return that 501(c)(3) public charities, private foundations, and most other tax-exempt organizations must file annually. The Form 990 is a public document. We ingest it primarily through the ProPublica Nonprofit Explorer feed, which mirrors the IRS Tax-Exempt Organization Search dataset. Original e-file XML and PDF copies of any return can be looked up directly at the IRS, ProPublica, or the Candid (formerly GuideStar) directory.

For every San Francisco organization listed above, the underlying Form 990 is available free of charge from the IRS Tax Exempt Organization Search, the ProPublica Nonprofit Explorer, or the Candid (GuideStar) directory.