Purpose: To determine the utility of running-only and rugby-specific, in-season sprint interval interventions in professional rugby league players. Methods: Thirty-one professional academy rugby players were assigned to a rugby-specific (SIT_r/s, n = 16) or running-only (SIT_r, n = 15) sprint interval training group. Measures of speed, power, change of direction ability, prone Yo-Yo Intermittent Recovery Test (Yo-Yo IR1) performance, and heart rate recovery were taken before and after the 2-week intervention as were submaximal responses to the prone Yo-Yo IR1. Internal, external, and perceptual responses were collected during SIT_r/s and SIT_r, with well-being and neuromuscular function assessed before each session. Results: Despite contrasting (possible to most likely) internal, external, and perceptual responses to the SIT interventions, possible to most likely within-group improvements in physical characteristics, heart rate recovery, and submaximal responses to the prone Yo-Yo IR1 were observed after both interventions. Between-group analysis favored the SIT_r/s intervention (trivial to moderate) for changes in 10-m sprint time, countermovement jump, change of direction, and medicine ball throw as well as submaximal (280–440 m) high metabolic power, PlayerLoad^™, and acceleration distance during the prone Yo-Yo IR1. Overall changes in well-being or neuromuscular function were unclear. Conclusions: Two weeks of SIT_r/s and SIT_r were effective for improving physical characteristics, heart rate recovery, and submaximal responses to the prone Yo-Yo IR1, with no clear change in well-being and neuromuscular function. Between-group analysis favored the SIT_r/s group, suggesting that the inclusion of sport-specific actions should be considered for in-season conditioning of rugby league players.