The aim of the present study was to examine whether combining strength and endurance training would promote better improvements in neuromuscular characteristics and functional abilities than endurance training alone in obese adolescent girls enrolled in a weight-reduction program. Twenty-four obese adolescent girls (12–15 years) volunteered to participate in a 9-month training program. Participants were allocated into two groups following either (i) combined training (endurance + strength; E+ST) or (ii) endurance training (ET) program. Absolute and specific maximal torque, muscle size, and maximal voluntary activation level (VA) of the knee extensor (KE) and plantar flexor (PF) muscles were assessed. Moreover, functional abilities such as balance and fatigability during a maximal isometric intermittent contraction test of the KE muscles were measured before and after the intervention. The force of the adductor pollicis (AP) muscles was used as a control to account for any effect of growth or mechanical unloading on neuromuscular properties and muscle size. While absolute and specific torque of the KE (+14.7 ± 12.1% and +14.4 ± 15.5%; p < 0.05) and PF (+19.2 ± 16.7% and +18.3 ± 17.5%; p < 0.001) muscles increased in the E+ST group, PF torque decreased, and KE torque did not change in the ET group (−22.6 ± 10.5% and −15.0 ± 17.2%; p < 0.001). Moreover, the VA of the KE muscles increased for the E+ST (+6.1 ± 5.6%; p < 0.01) group and decreased for the ET group (−5.4 ± 5.4%; p < 0.05). In contrast, VA remained similar in the PF muscles for both groups. The number of repetitions during the fatigability test increased in the ET group (38.4 ± 22.3 vs. 84.1 ± 33.3; p = 0.032) and was unchanged in the E+ST group (50.8 ± 14.1 vs. 54.2 ± 37.8), but it was associated with a higher force level. Moreover, balance improved in the E+ST group, but not in the ET group. To conclude, physical training combining strength and endurance training promoted larger improvement in neuromuscular characteristics and functional abilities than endurance training alone in obese adolescent girls. Greater neuromuscular adaptations resulting from the E+ST training may be beneficial for preserving or even increasing functional abilities and possibly induce greater engagement in the active lifestyle of obese adolescents. However, the endurance component seems necessary in training programs to reduce fatigability during daily living activities.