University students in the Czech Republic suffer from a low level of mental well-being. Research in other university student populations suggests that academic motivation, self-compassion, and self-criticism are strongly related to mental well-being. Students who are motivated to study, are kind toward themselves, and are less judgmental of themselves tend to have a high level of mental well-being. These relationships had not been evaluated in Czech students. Accordingly, this cross-sectional study aimed to evaluate the relationships between mental well-being, academic motivation (intrinsic motivation, extrinsic motivation, and amotivation), self-compassion (self-reassurance) and self-criticism (self-inadequacy and self-hate). Of 130 students approached, a convenience sampling of 119 psychology students at a university in the Czech Republic completed a survey regarding these constructs. Correlation, regression, and path analyses were conducted. Mental well-being was positively associated with intrinsic motivation and self-compassion, and negatively associated with amotivation and self-criticism. Self-compassion was identified as the strongest predictor of mental well-being. Lastly, intrinsic motivation mediated the pathway from self-compassion to mental well-being, but not the one from self-inadequacy to mental well-being, and the one from self-hate to mental well-being. Our findings can help educators to identify effective means to protect students’ mental well-being. Cultivating students’ self-compassion may be helpful to protect their mental well-being. University staff and educators in the Czech Republic need to consider ways to embed self-compassion training into their students’ programmes or university life.