Manual Resistance Training (MRT) has recently gained popularity and previous research suggested that MRT may be effective in improving muscular fitness in adults. As resistance training is an effective method to improve the fitness of adolescents, a variety of resistance training modalities have been applied for this population. The advantage of the MRT modality is the low cost due to the minimal equipment and space requirements. To compare the changes in fitness test scores between adolescents trained by the MRT and by traditional Weight Training (WT). One hundred seventy-four adolescents attending school-based physical education classes were pre-tested on their physical attributes by the Fitnessgram assessment tool, including the 1-mile run, curl-up, push-up, trunk lift, flexed arm hang, and modified pull-up tests. Classes of students were then assigned to either the MRT or WT protocol. Resistance training programs were used to complement the physical education classes and were applied for 30-45 minutes three times per week for 18 weeks. Students were tested prior to the intervention, at 9 weeks and at the end of the 18-week period. Data were analyzed using a General Linear Mixed Model Analysis with Tukey's post-hoc procedure for mean comparisons. At baseline, there were no significant differences between groups for age, height or weight (p > 0.05). However, adolescents in the WT group scored significantly higher in all measures of the Fitnessgram tool (p < 0.002). By 9-week both the MRT and WT groups showed significant improvements in the curl-up and trunk lift measures (p < 0.002) with the MRT group showing greater improvements. For the 1-mile run, push-up, flexed arm hang, and modified pull-up measures only the MRT group showed significant improvements (p < 0.005). Fitness scores for the WT group remained significantly higher for the 1-mile run and flexed arm hang tests (p < 0.012), but the significant group differences disappeared for the curl-up, trunk lift, push-up, and modified pull-up measures (p > 0.54). Neither group showed further significant improvement by 18-week in the 1-mile run, curl-up, trunk lift, flexed arm hang, or the modified pull-up measures (p > 0.09). In the push-up measure, only the WT group showed improvement from 9-week to 18-week (p = 0.019). At 18-week fitness scores were significantly higher in the WT group for the 1-mile run, curl-up, push-up, flexed arm hang and modified pull-up tests (p < 0.038). From baseline to 18-week both groups showed significant improvements in curl-up, trunk lift and push-up tests (p < 0.049), but only the MRT group showed significant improvements for the 1-mile run, flexed arm hang, and modified pull-up tests (p < 0.005). While the WT program was effective in improving some measures of adolescents' fitness, the MRT appeared to improve all measures. Adolescents trained by the MRT modality achieved greater improvements in the first half, but either only minimal improvements or some decrements in the second half of the 18-week intervention. Adolescents in the WT group generally made smaller but more progressive improvements throughout the 18-week intervention. Both the MRT and the traditional WT systems are appropriate for improving Fitnessgram scores within school-based physical education programs. The MRT modality appears to be effective in improving adolescents' fitness scores within 9 weeks of program application.