The imbalance in the hamstring to quadriceps (H:Q) ratio results in an increased susceptibility to hamstring strains and ACL injuries. Previous studies stipulated that compared to males the lower H:Q ratios may play an important role in the higher likelihood of ACL injuries in females. No known research has investigated the changes in H:Q ratios between males and females after an identical resistance training program. to compare the changes in hamstring and quadriceps strength and in the H:Q strength ratios between males and females following an identical resistance training program. Male (n = 16) and female (n = 17) college-age subjects with no history of lower-body injuries were recruited. All subjects were recreationally active but novice to lower-body resistance training. A 12-week resistance training program was applied consisting two 45-60 minutes sessions per week focusing on hamstring and quadriceps development. Subjects' hamstring and quadriceps strength of the dominant leg was assessed before and immediately after the intervention using an isokinetic dynamometer at 30°·s−1, 60°·s−1, and 180°·s−1 angular velocities. Maximal peak torque data were used to calculate quadriceps and hamstring strength relative to body weight, and the conventional and functional H:Q ratios. Pre- and post-training data were analyzed using an ANOVA with repeated measures. Males' concentric and eccentric hamstring strength and their concentric quadriceps strength improved significantly from baseline to 12-week at all angular velocities (p < 0.002). Females showed significant improvements in the concentric and eccentric hamstring strength at all angular velocities (p < 0.002), but only at 60°·s−1 for the concentric quadriceps strength (p < 0.019). Both males and females achieved the recommended 0.6 hamstring peak torque-to-body weight ratio by 12-week, but not the recommended 1.0 quadriceps peak torque-to-body weight ratio. Males showed modest and mostly non-significant improvements in conventional H:Q ratios, while females showed significant improvements at all angular velocities (p < 0.004). For the functional H:Q ratios, both males and females showed significant improvements from baseline to 12-week (p < 0.042), but females showed significantly greater improvements (p < 0.026). After the 12-week intervention, males and females reached 0.7-0.8 conventional and 1.1-1.4 functional H:Q ratios. While concentric and eccentric hamstring strength improved similarly in males and females, sex differences were observed in the improvement of concentric quadriceps strength as females showed only modest improvements. An important finding of the present study was that both males and females were able to meet and exceed the commonly recommended 0.6 conventional and 1.0 functional H:Q ratios after 12 weeks of resistance training. However, the 12-week intervention was not sufficient to improve subjects' relative quadriceps strength to that necessary for adequate functional performance. A 12-week systematic lower-body resistance training program may be effective in increasing the conventional and functional H:Q ratios above the recommended levels both in males and females. However, assessing the H:Q ratios does not fully describe the functional capacity of athletes, therefore the assessment of quadriceps and hamstring relative strength values are recommended in addition to the H:Q ratios.