This research aims to prioritize safety on the Muni system from a gender equity perspective and inform the Safety Equity Initiative of the San Francisco Municipal Transportation Agency (SFMTA). A mixed-method approach was used, including a survey of Muni transit riders (n = 1,613), to explore experiences of gender-based harassment and perceptions of safety while riding Muni. The findings reveal a significant prevalence of gender-based harassment, with 67 percent of respondents reporting experiences in the last six months. Perceptions of safety are low, with only 68 percent feeling safe during the daytime and 32 percent feeling safe at nighttime. Certain populations, including women, gender minorities, transit-dependent riders, and non-white riders, experience higher levels of harassment and lower perceptions of safety. Spatial analysis identifies harassment hotspots in downtown San Francisco and Mission Terrace. Reporting incidents is often hindered by reluctance, lack of awareness, and skepticism about the impact of reporting. The most desired safety improvements are transit ambassadors and increased lighting. Based on these findings, transformative recommendations are provided, categorized into three categories: service changes, infrastructure improvements, and campaigns/advocacy. This research contributes to knowledge about gender-based harassment in transit and informs the SFMTA's Safety Equity Initiative.