The aim of this investigation was to compare the changes in endurance running performance and physiological variables after a four-week period of high intensity interval training (HIIT) in either running or cycling in female athletes. Fourteen recreational female runners (age = 42 10 yr, height = 1.67 0.06 m, body mass = 61.6 10.4 kg, body mass index (BMI) = 22.2 3.4 kg.m^-2) were randomly allocated to one of two HIIT training groups: running (HIIT_run) or cycling (HIIT_bike). Each group performed two HIIT sessions per week for 4 weeks, which consisted of 6 x 2 min at 95% of maximal heart rate (HR_max) and 4 x 1 min all out efforts. Maximal oxygen consumption (VO_2max) in treadmill running increased significantly after the HIIT_run (p < 0.01, ES = 0.6) but remained unchanged in HIIT_bike. However, HIIT_bike improved average velocity in a 10 km running time trial (TT_run) (p < 0.05, ES = -0.4), whereas, no changes were found for the HIIT_run group. Analysing the first and last HIIT sessions, for HIIT_run only the average rate of perceived exertion (RPE_av) increased significantly, whereas, performance variables such as average heart rate (HR_av) and average pace (pace_av) remained unchanged. HIIT_bike enhanced significantly the average speed of HIIT sets (speed_av) and the peak power output (PPO) of the session, as well as, the RPE_av and delayed onset muscle soreness immediately after HIIT session (DOMS_post) were increased significantly. A regime of HIIT in cycling may evoke increases in female recreational runners’ power, which may be related with improvements in a 10 km TT_run independent of changes in aerobic capacity. This may be advantageous in order to avoid overuse running related injuries.