The deep fascia is intimately linked to skeletal muscle and may be involved in delayed onset muscle soreness (DOMS). The present study therefore explored the effect of eccentric exercise on fascia stiffness and its relation with DOMS. Healthy active male adults (n = 19, 27 ± 4 years) performed 6 x 10 maximal eccentric knee flexions using an isokinetic dynamometer. Before (baseline) as well as immediately (T0), 1 hour (T1), and each day up to 72 hours (T24 to T72) afterwards, shear wave elastography was used to measure the mechanical stiffness of the biceps femoris muscle and the overlying fascia. As a surrogate of DOMS, pain upon palpation was captured by means of a 100mm visual analogue scale. While muscle stiffness remained unchanged (p > 0.05), deep fascia stiffness increased from baseline to T24 (median: 18 kPa to 21.12 kPa, p = 0.017) and T72 (median: 18 kPa to 21.3 kPa, p = 0.001) post-exercise. Linear regression showed an association of stiffness changes at T24 and pressure pain at T72 (r2 = 0.22, p < 0.05). Maximal eccentric exercise leads to a stiffening of the fascia, which, in turn, is related to the magnitude of future DOMS. Upcoming research should therefore gauge the effectiveness of interventions modifying the mechanical properties of the connective tissue in order to accelerate recovery.