Jump performance is affected by warm-up intensity and body temperature, but the time course effects have not been thoroughly investigated. The purpose of this study was to investigate time course effects on jump performance after warm-up at different intensities. Nine male athletes (age: 20.9 ± 1.0 years; height: 1.75 ± 0.03 m; weight: 66.4 ± 6.3 kg; mean ± SD) volunteered for this study. The participants performed three warm-ups at different intensities: 15 min at 80% VO2 max, 15 min at 60% VO2 max, and no warm-up (control). After each warm-up, counter movement jump (CMJ) height, vastus lateralis temperature, heart rate and subjective fatigue level were measured at three intervals: immediately after warm-up, 10 min after, and 20 min after, respectively. Significant main effects and interactions were found for muscle temperature (intensity: p < 0.01, η2p = 0.909; time: p < 0.01, η2p = 0.898; interaction: p < 0.01, η2p = 0.917). There was a significant increase of muscle temperature from the baseline after warm-up, which lasted for 20 min after warm-up with 80% VO2 max and 60% VO2 max (p < 0.01). Muscle temperature was significantly higher with warm-up at 80% VO2 max than other conditions (P < 0.01). Significant main effects and interactions for CMJ height were found (intensity: p < 0.01, η2p = 0.762; time: p < 0.01, η2p = 0.810; interaction: p < 0.01, η2p = 0.696). Compared with the control conditions, CMJ height after 80% VO2 max and 60% VO2 max warm-ups were significantly higher (p < 0.01 and p < 0.05, respectively). CMJ height at 20 min after warm-up was significantly higher for 80% VO2 max warm-up than for 60% VO2 max warm-up (p < 0.01). However, CMJ height at 10 min after 60% VO2 max warm-up was not significantly different from the baseline (p < 0.05). These results showed that both high and moderate intensity warm-up can maintain an increase in muscle temperature for 20 min. Jump performance after high-intensity warm-up was increased for 20 min compared to a moderate intensity warm-up.