Abstract Background Primary dysmenorrhea leads to significant gynecological consultations, school absenteeism, disrupted daily activities, and adversely affects overall quality of life (QOL). Purpose This study compared the effects of aquatic exercise versus aerobic exercise on primary dysmenorrhea and QOL in adolescent females. Subjects and Methods Sixty adolescent females suffering from primary dysmenorrhea with moderate to severe intensity were distributed randomly and equally into two groups was registered at ClinicalTrials.gov (NCT06129708) the Registration Date, November 13, 2023; group A was treated by aquatic exercise for 12 weeks, while group B was treated by aerobic exercise for 12 weeks. Assessment of both groups before and after treatment involved evaluating dysmenorrhea severity using the WaLIDD Score, measuring pain intensity with the numeric pain rating scale (NPRS), determining pressure pain threshold (PPT) with an algometry, and evaluating the QOL using EuroQol—5 Dimension—3 Level (EQ‐5D‐3L) and EuroQol‐visual analog scale (EQ‐VAS). Results Both groups, A and B, experienced significant reductions in the WaLIDD score, NPRS, and all domains of EQ‐5D‐3L ( p < 0.05), coupled with significant increases in PPT and EQ‐VAS ( p < 0.05). Posttreatment comparisons between the groups showed insignificant differences in WaLIDD score, NPRS, and PPT ( p > 0.05). However, there was a significant decrease in EQ‐5D‐3L and a significant increase in EQ‐VAS, favoring group A ( p < 0.05). Conclusion Both aquatic and aerobic exercises are effective methods in primary dysmenorrhea management and QOL improvement in adolescent females, with a better effect of aquatic exercise in enhancing QOL.