Background: Higher education is a challenging context in which students particularly those endowed with a small array of resources are susceptible to suffer from burnout. To screen, identify, and support students that are at risk of burnout, psychometrically robust instruments are essential. To this end, we extended the validation of the German short version of the Maslach Burnout Inventory Student Survey (MBI-SS-KV) that allows measuring burnout among German-speaking university students. Method: We conducted a longitudinal study and analyzed the factorial validity, reliability, measurement invariance, and convergent as well as discriminant validity of the MBI-SS-KV in a sample of German university students (N = 1,435). Results: Our results replicated the original three-factor structure of the MBI-SS-KV. Yet, a bi-factor structure of the MBI-SS-KV composed of a general factor (i.e., student burnout) and three domain-specific factors (i.e., emotional exhaustion, cynicism, and reduced professional efficacy) revealed a comparable fit and was used for further analyses due to theoretical and methodological advantages. Based on the bi-factor structure of the MBI-SS-KV, nested models with increasing invariance constraints provided support for measurement invariance of this instrument across female and male university students and across time. Besides, the average variance extracted estimates and the comparisons of these estimates with shared variances demonstrated convergent and discriminant validity of the factors emotional exhaustion and cynicism, but not for the factor reduced professional efficacy. Conclusion: To sum up, we found that the MBI-SS-KV is a reliable and for the most part valid instrument for the assessment of student burnout in German higher education.