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Purpose: Delayed structural and functional recovery after a 20 km graded running race was analyzed with respect to the sex effect. Method s : Thirteen female and 14 male recreational runners completed the race and three test sessions: one before (PRE) and two after, once on Day 1 or 2 (D1‐2) and then on Day 3 or 4 (D3‐4). Muscle damage was assessed indirectly using ultrasonography to quantify changes in cross‐sectional area (CSA) of 10 lower‐limb muscles. Delayed onset of muscle soreness (DOMS) was assessed for three muscle groups. Functional recovery was quantified by kinetic analysis of a squat jump (SJ) and a drop jump (DJ) test performed on a sledge ergometer. Linear mixed models were used to assess control group reproducibility and recovery patterns according to sex. Results: Regardless of sex, DOMS peaked at D1‐2 for all muscle groups and resolved at D3‐4. CSA was increased in each muscle group until D3‐4, especially in the semimembranosus muscle. A specific increase was found in the short head of the biceps femoris in women. Regardless of sex, SJ and DJ performances declined up to D3‐4. Depending on the muscle, positive and/or negative correlations were found between structural and functional changes. Some of these were sex‐specific. Conclusion: Structural and functional recovery was incomplete in both sexes up to D3‐4, although DOMS had disappeared. More emphasis should be placed on hamstring muscle recovery. Highlighting the intermuscular compensations that can occur during multi‐joint testing tasks, the structural‐functional relationships were either positive or negative, muscle‐ and sex‐dependent. [ABSTRACT FROM AUTHOR]