Very little research has assessed the physical activity (PA) of university students in in Finland, and their associations with self-reported health complaints (HCs), whilst simultaneously accounting for a range of other potential confounders. Students at the University of Turku (1177) completed an online health and wellbeing questionnaire that assessed 22 physical and somatic HCs, and students' achievement of the international guidelines of four forms of PA (moderate, vigorous, moderate-to-vigorous and muscle strengthening PA; MPA, VPA, MVPA, MSPA respectively). We also explored the associations between HCs and PA, controlling for sociodemographic and health confounders (age, sex, year of study, marital status, accommodation during semesters, health awareness). Factor analysis reduced the HCs into three factors (psychological, pains/aches, circulatory/breathing). Bivariate relationships (no controlling for confounders) between these 3 factors and four forms of PA guideline achievement showed significant effects of achieving the PA guidelines against various groups of HCs, where more strenuous PA was associated with significantly less HCs in a step-ladder pattern. Multiple regression analyses (controlling for confounders) showed that achievement of PA guidelines was significantly independently associated with self-reported HCs scores in most cases. Psychological HCs were negatively associated with achieving any type of PA; pains/aches were negatively associated with achieving two types of PA or with achieving MSPA guidelines; and circulatory/breathing HCs were negatively associated with achieving the VPA guidelines only. This is the first study in Finland to examine such relationships, and highlights the critical role of PA for the health of these young adults. Programs and policies to strengthen and improve the PA of university students would be beneficial, recognizing the benefits of instilling life-long PA habits among this group of young adults.