Study aim: The purpose of this study was to evaluate neuromuscular adaptations in conscripts with different fitness levels (VO2max) during 8 weeks of military basic training (BT). Material and methods: Twenty-four male conscripts (18–21 years) were divided into two groups (Good Fitness [GF] and Low fitness [LF]) based on their VO2max at the beginning of BT. Body mass (BM), fat free mass (FFM) and Fat% were measured after 2, 4, and 7 weeks of training. VO2max, maximal isometric leg press force (MVC), H-reflex (Hmax/Mmax) at rest and V-wave (V/Mmax) during maximal isometric plantarflexion were measured from the soleus muscle at the beginning, after 5, and after 8 weeks of training. Results: FFM decreased significantly in LF after 7 weeks of training (–3.0 ± 1.7%, p < 0.001), which was not observed in GF. Both GF (6.9 ± 4.6%, p < 0.01) and LF (5.7 ± 4.6%, p < 0.01) showed improved VO2max after 5 weeks, with no changes during the last 3 weeks. A main effect of training was observed in decreased leg press MVC (–7.3 ± 9.3%, F = 4.899, p < 0.05), with no between-group differences. V-wave was significantly lower in LF during 5 (–37.9%, p < 0.05) and 8 (–44.9%, p < 0.05) weeks. Conclusion: Poor development of the neuromuscular system during BT suggests that explosive and/or maximal strength training should be added to the BT protocol for all conscripts regardless of fitness level. In addition, individualized training periodization should be considered to optimize the training load.