The aims of this study were twofold: (i) to examine differences in physical activity (PA) variables regarding the length of Physical Education (PE) lessons (45 vs. 90 min) and teaching methodology (Teaching Games for Understanding (TGfU) or hybrid TGfU-sports education (SE)); and (ii) to estimate the percentage of time spent in moderate-to-vigorous (MV) PA assessed via an accelerometer based on total step count, BMI, age, and sex, considering the pedagogical models and the class length. This study was carried out in three classes of invasion games in PE. Two classes were taught based on TGfU (44 students, 18 males, 12.6 ± 0.55), and one was taught based on a hybrid TGfU-SE (17 students, 9 males, 13.7 ± 0.90). The same students were assessed twice, first in a 45 min class and then in a 90 min class. The students’ MVPA was assessed using the Actigraph GT3X Activity Monitor. The results revealed significant differences in PA intensity regarding the length of the PE lesson (45 vs. 90 min) and the teaching methodology. The 45 min classes using TGfU were more intense and had less sedentary time than the 90 min classes. When using a hybrid TGfU-SE, the 90 min classes had higher intensities than the 45 min classes. Generally, when comparing the two types of pedagogical intervention, the TGfU model provided more active lessons and less sedentary time in class than a hybrid TGfU-SE. The TGfU model is more profitable for increasing MVPA in class. Due to the issues related to the organization and management of sports practice in class, several recommendations for maximizing MVPA in a hybrid TGfU-SE class must be considered.