Santa Ana Winds FC played in the SoCal Premier League from 2006 to 2011 before joining the National Premier Soccer League West Region-Flight Southwest Conference, also in 2011. The club played in the 2006–07 Raúl Briones Cup, Group B, that they shared with Morelos, PSA and OC United. Winds FC finished third behind Morelos and PSA.
Winds FC finished second in the NPSL Southwest Conference during their sole NPSL season, made the playoffs and fell in the first round to Hollywood United Hitmen, a national finalist that year, by a score of 3–1.
The club left the NPSL after one season due to a split between owners. One faction of ownership left and kept the Santa Ana Winds FC name, while forming a startup development league called the United Premier Soccer League, which was also founded in Santa Ana. The other faction of ownership continued to operate in the NPSL with the borrowed name Fullerton Rangers, and later called themselves Orange County Spartans, and then OC Pateadores, before disappearing from the NPSL. Winds FC shared the NPSL West – Flight Southwest conference with FC Hasental, Lancaster Rattlers (now FC Santa Clarita), San Diego Boca F.C. and the San Diego Flash.
Santa Ana Winds FC was a founding club of the United Premier Soccer League, established in 2011. The club has been playing UPSL, Open Cup and State Cup matches since in Lake Forest, California or Irvine, California consistently in the last few years, while attempting to find a home field in the City of Santa Ana. Winds FC has one UPSL Championship title, from the 2012–13 season, a league cup title (later named Admiral Cup) from 2014, two Western Conference, SoCal Division Championship titles and one Western Conference Championship title from the Spring-Summer 2018 season. The club played all of their Spring 2016 league matches at the Lake Forest Sports Complex in Lake Forest, approximately 17 miles away from the City of Santa Ana, and began scheduling UPSL summer/fall season matches at Santa Ana College in July 2016. Other fields where the club has played UPSL matches include the Orange County Great Park and Las Lomas Park, both in Irvine.
The club began playing UPSL matches at the SAUSD Sports Complex Stadium, also known as Valley Falcons Stadium, in April 2017. On December 7, 2017 Santa Ana Winds FC played their first UPSL league match at the newly built Championship Stadium at the Orange County Great Park against the LA Wolves, a game Winds FC won 3–1. Winds FC returned to Championship Stadium on January 7, 2018 in a playoff match against Orange County FC, a game Winds FC won 6–5 in penalty kicks. On January 13, Winds FC defeated the East Bay Stompers Juniors in the UPSL National Semi-final at Championship Stadium.