Teaching Games for Understanding (TGfU) is one of the pedagogical models used for increasing health through physical education (PE), being associated with several psychological benefits. However, only few studies have studied the effect of TGfU on physical fitness. This study aims at assessing the changes in students’ physical fitness after a six-month TGfU-based program with primary school children. A total of eight schools from the state of Sonora (Mexico) were randomly distributed into experimental (EG) and control group (CG). The final sample consisted of 188 pupils (100 boys, 88 girls; age = 10.22 ± 0.76 years) from the 5th and 6th grade. Employing a quasi-experimental design, physical fitness was assessed by means of the Eurofit test battery. At post-test, EG obtained significantly higher scores than CG in flexibility, abdominals, speed (p < 0.001), handgrip (p = 0.002), low-limb power (p = 0.032), and cardiorespiratory fitness (p = 0.048). Our findings suggest that TGfU can be a valid alternative to traditional methodologies not only when the aim of a PE unit is to stimulate the cognitive domain, but also for the development of physical fitness attributes that may help pupils develop in a comprehensive manner.