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, ⴄp2 = 0.09), timed rope skipping (F = 27.87, p < 0.001, ⴄp2 = 0.14), agility T-test (F = 26.01, p < 0.001, ⴄp2 = 0.13), and standing long jump (F = 16.43, p < 0.001, ⴄp2 = 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.