Motor skill learning is a fundamental aspect of human behavior based on the calibration of internal models via sensory information such as proprioception. Some conditions, as exercise-induced muscle damage (EIMD), disrupt proprioceptive information, and may cause learning impairment. Such possible relation between EIMD and motor skill learning has not yet been investigated and it is the aim of this study. For this purpose, thirty male university students (19.3 ± 1.8 years) were equally assigned to two groups: EIMD and CON group. The EIMD group received a treatment to induce muscle damage consisting of a weight lifting protocol directed to the agonist muscles related to the task prior to the pretest and to the learning sessions. EIMD was verified and compared between groups and along the process (0–168 h) by means of the degree of delayed onset muscle soreness (DOMS), perceived total quality recovery and maximal isometric strength (MIS). To investigate motor skill learning, both groups practiced a dart throwing task for four sessions with 150 trials in each session. Recovery status and DOMS were recovered at 96 h in the EIMD group, and MIS was not recovered throughout 168 h. In contrast, muscle damage parameters were not altered across 168 h in the CON group. Accuracy and consistency were compared within and between groups in a pretest posttest design. The EIMD group showed less accurate and consistent results on the long term (delayed posttest). Results confirmed our hypothesis that EIMD, a common condition in sports and in rehab practices, may hinder motor skill learning, possibly due to neurological aspects such as proprioceptive information, its relation to central nervous system reorganization and internal model consolidation.