This study explored the development of neuromuscular fatigue responses during progressive cycling exercise. The sample comprised 32 participants aged 22.0 ± 0.54 years who were assigned into three groups: endurance-trained group (END, triathletes, n = 10), strength-trained group (STR, body-builders, n = 10), and control group (CON, recreationally active students, n = 12). The incremental cycling exercise was performed using a progressive protocol starting with a 3 min resting measurement and then 50 W workload with subsequent constant increments of 50 W every 3 minutes until 200 W. Surface electromyography (SEMG) of rectus femoris muscles was recorded during the final 30 s of each of the four workloads. During the final 15 s of each workload, participants rated their overall perception of effort using the 20-point RPE scale. Post-hoc Tukey’s HSD testing showed significant differences between END and STR groups in MF and MPF across all workloads (p < 0.001 and p < 0.01, respectively). Athletes from END group had significantly lower AEMG responses than those from STR (p = 0.0093) and CON group (p = 0.0006). Increasing RPE points from 50 to 200 W were significantly higher in STR than in END group (p < 0.001). In conclusion, there is a significant variation in neuromuscular fatigue profiles between athletes with different training backgrounds when a cycling exercise is applied. The approximately linear trend of the SEMG and RPE values of both groups of athletes with increasing workload support the increased skeletal muscle recruitment with perceived exertion or fatiguing effect.