Background: Fitness is a powerful marker of health associated with physical activity (PA) in university students. However, insufficient PA is a serious health concern among university students. Active commuting provides an opportunity for increased PA levels. Therefore, the aims of this study were (a) to describe the mode of commuting, PA and fitness in university students; (b) to analyze the associations of mode of commuting with PA and fitness; and c) to analyze the relationship between mode of commuting, PA recommendations and fitness. Methods: This was a cross-sectional study. A total of 1257 university students (52.4% women) participated (22.4 ± 5.6 years old). Results: Public commuting was the main mode to and from university. Active and public commuters were more likely to meet the PA recommendations and reported higher muscular strength than those using private commuting. Active and public commuters who met PA recommendations present the highest fitness in most of its components. Conclusions: Achieving the PA recommendations was more relevant than adopting an active mode of commuting in order to have better fitness. Further research targeting a broader understanding of the mode of commuting, PA levels and fitness in university students is needed.