The deal for Girma is for three years, which includes this season, plus an option year that the team has exercised.
"Naomi has been an integral piece of the Wave's success on and off the field since she joined the club," said Wave general manager Molly Downtain.
"She has proven that she is one of the top players in this league, and we are thrilled to have her continue to lead our club. Securing her long-term future was a priority for the club, and we are pleased that we were able to reach this agreement as we know Naomi will play a crucial role in the Wave for years to come."
Picked in the 2022 NWSL Draft by San Diego in their inaugural season, Girma quickly made a name for herself after winning both the 2022 NWSL Rookie and Defender of the Year awards, making her the first league history to earn two individual season awards in a rookie year.
"The start to my professional journey has been so rewarding here in San Diego," said Girma.
"Since being drafted, everyone at the Wave has made San Diego feel like home. My goal has always been to win championships for this city and raise the trophies with my team. I can't wait to play in front of the Sirens [supporters group] and fans for years to come."
With the 23-year-old defender starting in every game so far this season, the Wave are currently sitting at the top of the NWSL standings. On Saturday, Girma and her teammates will host California rivals Angel City FC at San Diego's Snapdragon Stadium.
Looking ahead to the Women's World Cup that begins next month in Australia and New Zealand, the former Stanford University player is expected to be a key figure for a USWNT side that will be aiming for a third consecutive title. In the group stage, head coach Vlatko Andonovski and his players will face Vietnam (July 22), the Netherlands (July 27), and Portugal (Aug. 1).
Girma has collected 15 caps with the USWNT after making her senior debut in April of last year.