Children have received much attention in recent years, as many studies have shown that their physical fitness level is on the decline. Physical education, as a compulsory curriculum, can play a monumental role in contributing to students' participation in physical activities and the enhancement of their physical fitness. The aim of this study is to examine the effects of a 12-week physical functional training intervention program on students' physical fitness. A total of 180 primary school students (7-12 years) were invited to participate in this study, 90 of whom participated in physical education classes that included 10 min of physical functional training, and the remaining 90 were in a control group that participated in traditional physical education classes. After 12 weeks, the 50-m sprint (F = 18.05, p < 0.001, ηp2 = 0.09), timed rope skipping (F = 27.87, p < 0.001, ηp2 = 0.14), agility T-test (F = 26.01, p < 0.001, ηp2 = 0.13), and standing long jump (F = 16.43, p < 0.001, ηp2 = 0.08) were all improved, but not the sit-and-reach (F = 0.70, p = 0.405). The results showed that physical education incorporating physical functional training can effectively promote some parameters of students' physical fitness, while at the same time providing a new and alternative idea for improving students' physical fitness in physical education.