Mediterranean fruit fly (Medfly) Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) is a globally significant economic pest for which lure based trapping can be used to monitor established populations and for surveillance. Either female- or male-targeted traps can be used; however, recommendations on which to apply are inconsistent and many programs rely on male-targeted traps. Here, we compare the performance of male-targeted traps (Lynfield Trap with Trimedlure) and female-targeted traps (Biotrap Globe trap with the 3-component lure—TMA Plus) in apple orchards in south-west Western Australia over 2 years (September 2019 to September 2021). Male-targeted traps caught more Medflies overall than female-targeted traps, although the difference was minor. However, female-targeted traps were better at attracting Medfly early in the season when populations were small; and were more likely to capture at least one fly when their paired male-targeted trap caught none. Conversely, male-targeted traps were more likely to capture Medflies late in the season and were more likely to catch high numbers of Medflies. Consequently, female-targeted traps may be better at detecting Medfly early in the season, and male-targeted traps may be better at detecting Medfly abundance late in the season, at least in apple orchards. Our results suggest that either or both trap-types could be used for monitoring Medfly populations, with the optimal solution being dependent on the intended application.