The San Diego chapter of the Ninety-Nines was chartered on September 14th, 1946. Before its formation, local members were part of the
Los Angeles chapter but decided to establish a chapter closer to home. The first gathering of San Diego area Ninety-Nines took place at a dirt airstrip near Sweetwater/Otay Mesa, marking the beginning of the chapter. Initially formed by ten members, the chapter quickly grew. By the 1970s, the membership had expanded so much that some members branched off to form the El Cajon Valley chapter. In the 1980s, others established the Mission Bay chapter to better serve their areas of the county.

In the early 2000s, these splintered chapters decided to reunite, leading to the formation of the present-day San Diego chapter. A pivotal moment came when longtime member Fran Bera secured a large hangar at Gillespie Field, which became the chapter's new meeting place. Fondly known as “Fran’s Hangar,” it could easily accommodate up to 75 people and became the heart of the chapter’s activities. Fran was a dedicated member for decades, and her passing was deeply felt by all.