The functional FABP2 Ala54Thr polymorphism (rs1799883) is strongly associated with lipid and carbohydrate metabolism, although the function of its potential modifying effect on training-induced changes in obesity-related parameters is still unknown. The aim of the present study was to investigate the influence of the Ala54Thr polymorphism on post-training changes of selected body mass and body composition measurements, as well as with biochemical parameters of energy metabolism. Accordingly, alleles and genotypes distribution in a group of 168 young, nonobese Caucasian women measured for chosen body composition parameters, lipid profile, and glucose levels before and after the completion of a 12-week aerobic training program were studied. Although the obtained results showed changes in body mass, BMI, FM, %FM, FFM, TBW, HDL-C, and glucose levels during the training program, none of the examined parameters changed significantly across the FABP2 genotypes. Instead, we found a main effect of genotype on BMI (p = 0.033), with carriers of the Thr54 allele having a higher BMI during the whole study period compared with the Ala54 carriers. We confirm that the FABP2 Ala54Thr polymorphism may help identify women at risk for overweight and obesity. However, we did not notice evidence of an interaction between physical activity and the Ala54Thr polymorphism on the examined parameters.