Objectives Analyze whether there are immediate changes in peak soleus activation and peak hindfoot eversion after short-foot exercise (SFE) in runners with medial tibial stress syndrome (MTSS). Secondarily, establish differences in peak soleus activation and peak hindfoot eversion between asymptomatic individuals and those presenting MTSS. Design Quasi-experimental study. Setting University Laboratory. Participants Thirty-two runners participated: 16 with MTSS and 16 in the no-pain group (NPG). Main outcome measures Soleus activation was measured using electromyography, and hindfoot eversion via 3D kinematic analysis. Participants performed SFE, and running data were collected at 9,12 and 15 km/h pre- and post-intervention. Results SFE reduced peak soleus activation at 9 (p = 0.017) and 15 km/h (p = 0.019) for the MTSS group and at 15 km/h (p < 0.001) for the NPG, suggesting improved neuromuscular efficiency and potentially reduced tibial stress. SFE did not significantly affect peak hindfoot eversion. Significant correlations were found between ankle dorsiflexion range of motion and muscle activation (r = 0.585 to 0.849, p < 0.05). These findings suggest SFE could improve neuromuscular efficiency and reduce tibial stress, and highlights ankle flexibility's role in muscle activation. Conclusions SFE significantly reduces soleus activation, potentially improving neuromuscular efficiency and decreasing tibial stress.