This study aimed to determine the effects of two training methods on the strength and mobility of trunk muscles in primary school girls. The sample of participants included 596 girls aged 11 to 15. The participants were randomly assigned to two groups: 1) an experimental group (n = 314) that performed a functional training (FT) program; 2) a control group (n = 282) that performed regular Physical Education (PE) classes. The experimental program was implemented during regular PE classes over a period of 16 weeks, where 3 training sessions were conducted per week, lasting 45 minutes each. The FitnessGram battery of tests was used to estimate the strength and mobility of trunk muscles at the initial and the final measurement. The following tests were used: Curl up, Incline push-ups, and dynamic and static Trunk lift tests. The results of the two-factor ANOVA showed significant (p < 0.001) improvements in each test for both groups. The magnitude of the effect size ranged from medium to large and differed between the methods in all tests except for abdominal muscle strength. These findings indicate that both training programs are beneficial for developing trunk muscle strength and mobility in primary school girls. Future research should consider investigating differences between the methods in primary school students.