This study investigated the sex influence on the acute and delayed fatigue effects of a 20 km graded running race. Eighteen recreational runners, 10 women and 8 men, completed the race. The testing protocol included five sessions: a week before the race (PRE), 35 ± 15 min after (POST), 2 h, 2 and 4 days (2D and 4D) later. Each session included uni- and bilateral maximal isometric voluntary contractions of the knee extensors (MVC), a squat jump (SJ), and a drop jump (DJ). Acute and delayed muscle soreness (DOMS) were evaluated for the quadriceps, hamstring and triceps surae muscle groups. The 2D and 4D sessions included also a horizontal force-velocity test (HF-V) performed under five resistive conditions. For each test, a set of key variables was computed to characterize the lower limb functional recovery. Mixed ANOVA analyses revealed significant (sex × time) interactions, with larger acute drops for men in MVCs and earlier recovery for women in the bilateral MVC ( p < 0.001) and DJ ( p < 0.05) tests. Only women reported DOMS for the hamstrings at 2D ( p < 0.001) and showed small improvements in pure concentric SJ ( p < 0.05) and HF-V ( p < 0.01) tests at 4D. As expected, DOMS disappeared prior to the complete functional recovery. These results confirmed the combined influence of testing task and sex on the functional recovery pattern while supporting a lesser and faster recovery in women. The originality of this study lies in the complexity and sex-dependence of the functional recovery pattern revealed by a multiple factorial analysis which was used to identify the most discriminating tests and variables in the recovery pattern. The obtained clusters highlighted some recovery profiles associated with greater risks of injury when starting to run again. However, the lack of sex × time interaction for normalized values emphasizes the major influence of men’s initially higher functional values compared to women.