An acute bout of distance running decreases Achilles tendon CSA. The purpose of this study was to examine if three-week stretch training of the Achilles tendon alters the Achilles tendon thinning response to running. Thirty-three recreational runners were divided into a control group (n = 17) and an intervention group (n = 16). The intervention included a three-week soleus stretch (knee flexed) and gastrocnemius stretch (knee extended). Three gastrocnemius stretches and three soleus stretches were performed each day, six days per week. Stretches were held for 30 s per repetition for a total duration of 180 s per leg per day. Achilles tendon CSA and range of motion measures were completed pre and post-run before and after the three-week stretching intervention. The runs prior to and following the three-week stretch training intervention both resulted in a 6% decrease in Achilles tendon CSA (p < 0.0001). There was no interaction across time between control and intervention groups in CSA (p = 0.446). Only the intervention group experienced a significant increase in dorsiflexion range of motion following the stretch training (p = 0.009). We therefore conclude that even when an increased dorsiflexion range of motion occurs, three weeks of triceps surae stretching does not alter the response of the Achilles tendon CSA.