Warm-up protocols with high intensities before continuous running provide potential benefits for middle-distance runners. Nevertheless, the effect of high-intensity warm-ups on long-distance runners remains unclear. The purpose of this study was to verify the effect of a high-intensity warm-up protocol on 5000 m performance in trained runners. Thirteen male runners (34 ± 10 years, 62 ± 6 kg, 62.7 ± 5.5 ml/kg/min) performed two 5000 m time trials, preceded by two different warm-ups. One high-intensity warm up (HIWU: 1x 500 m (70% of the running intensity) + 3x 250 m (100% of the running intensity) and one low-intensity warm up (LIWU: 1x 500 m (70% of the running intensity) + 3x 250 m (70% of the running intensity)), where the running intensities were calculated using the results obtained in the Cooper test. Physiological and metabolic responses, and endurance running performance parameters, were evaluated by the Counter Movement Jump (CMJ), running rating of perceived exertion (RPE), blood lactate concentration (BLa), and performance running. Total time for the 5000 m was lower using HIWU when compared to LIWU (1141.4 ± 110.4 s vs. 1147.8 ± 111.0 s; p = 0.03; Hedges' g = 0.66). The HIWU warm-up led to an improvement in pacing strategy during the time trial. After warm-up protocols, the performance on the CMJ was improved only when applying HIWU (p = 0.008). Post warm-up BLa was significantly higher for HIWU vs. LIWU (3.5 ± 1.0 mmol·L^-1 vs. 2.3 ± 1.0 mmol·L^-1; p = 0.02), with similar behavior for the RPE (p = 0.002), internal load of the session (p = 0.03). The study showed that a high-intensity warm-up protocol can improve performance in the 5000 m in trained endurance runners.