Background: Primary Dysmenorrhea is one of the most common gynecological conditions among young women; it is characterized by menstrual pain with the absence of pelvic pathology. However, little research has been done on its psychological and academic impact, especially among female university students. The purpose of this study is to determine the relationship between primary dysmenorrhea and academic performance and mental health in a sample of female university students in Jordan. Methods: This online, cross-sectional survey was conducted between August and November of 2025. 492 female university students at Mutah University, Jordan, completed a self-structured questionnaire on sociodemographic and menstrual history. The severity of primary dysmenorrhea (PD) was assessed using the WaLIDD scale (Working ability, Location, Intensity, Days of Pain), while psychological well-being was assessed using Depression, Anxiety, and Stress Scale (DASS-21). The self-reported cumulative grade point average (CGPA) was used to assess academic performance. Descriptive and inferential statistics were used to analyze the data, with a significance level of p < 0.05. Results: Participants were predominantly (91.1%) between the ages of 18 and 24, single (84.8%), and Jordanians (94.7%). PD was reported by the majority, with 73.8% reporting pain lasting 1-2 days, and 43.3% skipping classes due to menstrual pain. Age, sleep duration, education level, dietary habits, analgesic use, pain duration, and family history of dysmenorrhea significantly predicted PD severity (final model R² = 25.4%, p < 0.001). Mean DASS-21 scores indicated mild level of depression (M = 1.11, SD = 1.55), anxiety (M = 1.15, SD = 1.38), and stress (M = 0.82, SD = 1.21). Conclusion: Primary dysmenorrhea is highly prevalent and has an impact on academic achievement among Jordanian female university students. The findings on the predictors offer targeted interventions and the need for in-campus health services to improve students' menstrual health and academic achievement.