Purpose To investigate the effect of warmup by application of the thermal agent Deep Heat (DH) on muscle mechanical properties using magnetic resonance elastography (MRE) at 3T before and after exercise-induced muscle damage (EIMD). Materials and Methods Twenty male participants performed an individualized protocol designed to induce EIMD in the quadriceps. DH was applied to the thigh in 50% of the participants before exercise. MRE, T2-weighted MRI, maximal voluntary contraction (MVC), creatine kinase (CK) concentration, and muscle soreness were measured before and after the protocol to assess EIMD effects. Five participants were excluded: four having not experienced EIMD and one due to incidental findings. Results Total workload performed during the EIMD protocol was greater in the DH group than the control group (P < 0.03), despite no significant differences in baseline MVC (P = 0.23). Shear stiffness |G*| increased in the rectus femoris (RF) muscle in both groups (P < 0.03); however, DH was not a significant between-group factor (P = 0.15). MVC values returned to baseline faster in the DH group (5 days) than the control group (7 days). Participants who displayed hyperintensity on T2-weighted images had a greater stiffness increase following damage than those without: RF; 0.61 kPa vs. 0.15 kPa, P < 0.006, vastus intermedius; 0.34 kPa vs. 0.03 kPa, P = 0.06. Conclusion EIMD produces increased muscle stiffness as measured by MRE, with the change in |G*| significantly increased when T2 hyperintensity was present. DH did not affect CK concentration or soreness; however, DH participants produced greater workload during the EIMD protocol and exhibited accelerated MVC recovery.