Background: Gender differences in personal discrimination experience, burnout, and job stress among physiotherapists and occupational therapists are considered as associated factors of job loss, poor job quality, high turnover, and economic losses due to the outflow of medical personnel. Thus, the purpose of this study is to analyze the level of burnout, personal discrimination experience, and job stress according to gender differences for young physiotherapists and occupational therapists. Furthermore, we used regression analyses to determine the contribution of gender differences in personal discrimination experience and job stress to self-reported burnout, considering gender and two age groups (younger than 30 years old vs. 30 years old and over). Methods: A total of 325 professional physiotherapists and occupational therapists were part of this study (n = 325; male n = 131; female n = 194. Age: 20–29 years old, n = 178; ≥30 years old, n = 147). Data were collected using a questionnaire including our three study variables (scales: the Maslach Burnout Inventory (MBI), a modified version of the gender section of the Medical School Graduation Questionnaire from the Association of American Medical Colleges; and the Korean version of the Job Content Questionnaire (JCQ)). Further, data on socio-demographic factors, job-related factors, health-related factors, and subjective job satisfaction were also collected. Results: There were significant positive correlations between job stress and gender differences in personal discrimination experience and job stress and burnout in women 30 years old and over. Personal experience of gender discrimination (β = 0.179, p = 0.015) and job stress (β = 0.162, p = 0.028) explained a significant 42.4% of the variance in burnout in the case of younger female participants (20–29 years old). However, this model did not explain a significant amount of the variance in burnout in the case of younger male participants (R2 = 0.156, p = 0.072). Regarding participants aged 30 years and over, our results showed that only job stress (but no personal experience of gender discrimination) was a relevant predictor for both males (β = 0.471, p < 0.001) and females (β = 0.373, p = 0.001). Conclusion: In this study, female therapists showed higher levels of burnout than male therapists. In particular, personal discrimination experience and job stress significantly contributed to burnout in younger female therapists while job stress was the most relevant predictor variable of burnout for both males (under 30 years old and 30 years old and over) and females in their thirties and beyond. For young female physiotherapists and occupational therapists, safe working environments should be created to reduce work-related mental burdens. It is also necessary to consider policies and regulations that can prevent job stress for therapists and measures that can positively resolve the unavoidable job stress.