Active-learning approaches to teaching introductory physics have been found to improve student learning and affective gains on short-term outcomes [S. Freeman et al., "Proc. Natl. Acad. Sci. U.S.A. 111," 8410 (2014)]; however, whether or not the benefits of active learning impact women to the same degree as men has been a point of concern [A. Madsen, S. B. McKagan, and E. C. Sayre, "Phys. Rev. ST Phys. Educ. Res." 9, 020121 (2013)]. Further, the long-term impacts of active-learning experiences are also understudied. At Florida International University, a Hispanic-majority institution, we have implemented Modeling Instruction (MI) and the Integrated Science Learning Environment (ISLE) in introductory physics classes for the past decade. In this empirical paper, we report on a longitudinal investigation of student performance and persistence in upper level physics courses after having previously experienced MI or ISLE in their introductory physics courses, and disaggregate students by gender. Using survival analysis methods, we find women who declare physics as a major are more likely than men to graduate with a physics degree. Women are also just as likely as men to pass through the upper division courses, with the highest failure risk for both men and women occurring in the first semester of upper-division course taking. These results reinforce the need to expand considerations of performance outcomes to be longitudinal to measure the effectiveness of the entire physics experience. [This paper is part of the Focused Collection on Gender in Physics.]