"I will sadly not be back," Sowers told Cam Inman of the Bay Area News Group with her Niners contract set to expire.
The 34-year-old Kansas native spent four years with the organization. She was hired as a seasonal offensive assistant in 2017 and was then elevated to a full-time role beginning in 2019.
"I think it's important to understand that the path you were meant to take is more often than not .. the path that was least expected," she wrote Thursday on Instagram. "But that is the beauty in your story and you will always control the narrative."
The 49ers haven't commented on Sowers' departure, which Inman noted has been standard policy with departing assistants since Kyle Shanahan was hired as head coach in 2017.
Before arriving in San Francisco, the Central Missouri product played football in the Women's Football Alliance and as a member of the United States women's national team. She helped the U.S. win the 2013 IFAF Women's World Championship in Finland.
Her NFL career started as a training camp assistant for the Atlanta Falcons in 2016, with a focus on wide receivers. She remained with the Falcons as a scouting intern before joining the Niners.
Sowers became the first woman to coach in the Super Bowl in February when San Francisco suffered a 31-20 loss to the Kansas City Chiefs in Super Bowl LIV.