The extrinsic foot muscles are essentially for controlling the movement path but our knowledge of their behavior during prolonged running is still very limited. Therefore, this study analyzed the time-course of muscle activation using T2 mapping during 75 min of running. In this prospective study, 19 recreational active runners completed 75 min of treadmill running at a constant speed. Interleaved T2 mapping sequences were acquired and segmented at timepoints 0, 2.5, 5, 10, 15, 45, and 75 min. ANOVA for repeated measurements followed by a Tukey post hoc test and Pearson correlation between running speed and initial signal increase at 2.5 min were calculated. All muscles showed a significant signal increase between baseline and 2.5 min (e.g. medial gastrocnemius: + 15.48%; p < 0.01). This was followed by a plateau phase till 15 min for all but the extensor digitorum longus muscle and a significant decrease at 45 or 75 min for all muscles (all p < 0.05). Correlation between running speed and signal increase was negative for all muscles and significant for both gastrocnemii (e.g. medial: r = − 0.57, p = 0.0104) and soleus (r = − 0.47, p = 0.0412). The decrease of relaxation times times in the later running phases was less pronounced for faster runners (≥ 10 km/h). T2 relaxation times do not only decrease after cessation of exercise but already during prolonged running. The lesser initial increase and later decrease in faster runners may indicate training induced changes.