Previous studies suggest that marathon running induces lower extremity muscle damage. This study aimed to examine inter- and intramuscular differences in hamstring muscle damage after a marathon using transverse relaxation time (T2)-weighted magnetic resonance images (MRI). 20 healthy collegiate marathon runners (15 males) were recruited for this study. T2-MRI was performed before (PRE) and at 1 (D1), 3 (D3), and 8 days (D8) after marathon, and the T2 values of each hamstring muscle at the distal, middle, and proximal sites were calculated. Results indicated that no significant intermuscular differences in T2 changes were observed and that, regardless of muscle, the T2 values of the distal and middle sites increased significantly at D1 and D3 and recovered at D8, although those values of the proximal site remained constant. T2 significantly increased at distal and middle sites of the biceps femoris long head on D1 (p = 0.030 and p = 0.004, respectively) and D3 (p = 0.007 and p = 0.041, respectively), distal biceps femoris short head on D1 (p = 0.036), distal semitendinosus on D1 (p = 0.047) and D3 (p = 0.010), middle semitendinosus on D1 (p = 0.005), and distal and middle sites of the semimembranosus on D1 (p = 0.008 and p = 0.040, respectively) and D3 (p = 0.002 and p = 0.018, respectively). These results suggest that the distal and middle sites of the hamstring muscles are more susceptible to damage induced by running a full marathon. Conditioning that focuses on the distal and middle sites of the hamstring muscles may be more useful in improving recovery strategies after prolonged running.