Established in 1971, Raphael House began as an emergency shelter for single mothers and their children. A small group of committed volunteers rented a location from the city to serve the families. However, they quickly outgrew the limited space, and Mrs. Ella Rigney, the founder, was charged with finding a larger facility. Relocating to the former Golden Gate Hospital at 1065 Sutter Street, the facility was renovated to accommodate 51 beds in 17 bedrooms. Opening Thanksgiving week, 1977, Raphael House became the first homeless shelter for families in Northern California. Since its inception, Raphael House has provided over 20,000 families personalized family-centered solutions to build brighter, independent futures.

In 1991, Raphael House became incorporated. Shortly after, the staff formulated the Bridge aftercare program, designed to provide ongoing services to former resident families who had moved on to stable housing. In direct response to a growing need in the community, Raphael House eventually expanded to 70 beds in 23 bedrooms. Overtime, Raphael House also greatly expanded its educational and supportive programming for children.

Throughout its history, Raphael House has received several prestigious management awards, including the John R. May Award from the San Francisco Foundation, the Management Center's Award for Excellence in Non-Profit Management and the Sara Lee Leadership Award.