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 (HIITrun) or cycling (HIITbike). Each group performed two HIIT sessions per week for 4 weeks, which consisted of 6 x 2 min at 95% of maximal heart rate (HRmax) and 4 x 1 min all out efforts. Maximal oxygen consumption (VO2max) in treadmill running increased significantly after the HIITrun (p < 0.01, ES = 0.6) but remained unchanged in HIITbike. However, HIITbike improved average velocity in a 10 km running time trial (TTrun) (p < 0.05, ES = -0.4), whereas, no changes were found for the HIITrun group. Analysing the first and last HIIT sessions, for HIITrun only the average rate of perceived exertion (RPEav) increased significantly, whereas, performance variables such as average heart rate (HRav) and average pace (paceav) remained unchanged. HIITbike enhanced significantly the average speed of HIIT sets (speedav) and the peak power output (PPO) of the session, as well as, the RPEav and delayed onset muscle soreness immediately after HIIT session (DOMSpost) 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 TTrun independent of changes in aerobic capacity. This may be advantageous in order to avoid overuse running related injuries. Key points This article observes the effects of a HIIT program in two different modes, i.e. cycling and running, in a hardly investigated population, recreational middle-age female runners. The analysis of physiological variables in a HIIT session, maximal test and 10 km time trial run performance.