There is a paucity of data examining the impact of high-intensity interval hypoxic training (IHT) on intermittent running performance. This study assessed the effects of IHT on 17 amateur Australian Footballers, who completed 8 interval treadmill running sessions (IHT [FIO2 = 15.1%] or PLACEBO) over 4 weeks, in addition to normoxic football (2 per week) and resistance (2 per week) training sessions. To match relative training intensity, absolute IHT intensity reduced by 6% of normoxic vV[Combining Dot Above]O2peak compared with PLACEBO. Before and after the intervention, performance was assessed by Yo-Yo intermittent recovery test level 2 (Yo-Yo IR2) and a self-paced team sport running protocol. Standardized effect size statistics were calculated using Cohen's d to compare between the interventions. Compared with PLACEBO, IHT subjects experienced (a) smaller improvements in Yo-Yo IR2 performance (Cohen's d = -0.42 [-0.82 to -0.02; 90% confidence interval]); (b) similar increases in high-intensity running distance during the team sport protocol (d = 0.17 [-0.50 to 0.84]); and (c) greater improvements in total distance (d = 0.72 [0.33-1.10]) and distance covered during low-intensity activity (d = 0.59 [-0.07 to 1.11]) during the team sport protocol. The lower absolute training intensity of IHT may explain the smaller improvements in Yo-Yo IR2 performance in the hypoxic group. Conversely, the data from the self-paced protocol suggest that IHT may positively influence pacing strategies in team sport athletes. In conclusion, IHT alters pacing strategies in team sport athletes (i.e., increased distance covered during low-intensity activity). However, IHT leads to smaller improvements in externally paced high-intensity intermittent running performance (i.e., Yo-Yo IR2), which may be related to a reduced absolute training intensity during IHT sessions.