Following is a list of notable non-profit organizations headquartered in the city of Jacksonville, Florida. 

 Jacksonville University
Alfred I. duPont Testamentary Trust
Alliance for the Lost Boys of Sudan Florida
Baptist Health
Boselli Foundation
Brothers Fighting Against Mental Health 
Clara White Mission
Communities In Schools of Jacksonville
Community Hospice of Northeast Florida
Dreams Come True
FreshMinistries
Gator Bowl Association
HabiJax
Hubbard House
Jacksonville Arboretum & Gardens
Jacksonville Civic Council
MaliVai Washington Kids Foundation
Nemours Children's Clinic
Otis Smith Kids Foundation
Second Harvest North Florida 
St. Vincent's HealthCare
Sulzbacher Center
Tom Coughlin Jay Fund Foundation
UF Health Jacksonville

Lists of organizations based in the United States
Jacksonville, Florida-related lists