The objective of this research was to analyze the impact of an intervention program performed by a specialist in physical education (PE) to contribute to the development of motor competence (MC) in pre-school children with motor development problems. The sample consisted of 28 children (12 from the intervention group and 16 from the control group) aged between 4.1 and 5.9 years (mean = 4.71 ± 0.54) who were in the fifth and sixth grades of pre-school education in two schools from Lugo, Spain. The Movement Assessment Battery for Children-2 (MABC-2) was used for data collection. The data revealed that, in the pre- and post-test intervention groups, there are statistically significant differences in manual dexterity (p < 0.001; d = 2.63), aiming and catching (p < 0.002; d = 1.13), balance (p < 0.001; d = 1.68), total test score (p < 0.001; d = 3.30) and total percentile score (p < 0.001; d = 1.88). Between the control and intervention post-test groups, significant differences were found in manual dexterity (p = 0.015; η2 = 0.22), aiming and catching (p = 0.003; η2 = 0.32), balance (p = 0.050; η2 = 0.15), total test score (p < 0.001; η2 = 0.47) and total percentile score (p < 0.001; η2 = 0.48). Based on the results obtained, a specific MC program implemented by a PE specialist contributed to the improvement of manual dexterity, aiming and catching and balance, as well as a better percentile in the general MC of pre-school children diagnosed with motor skill problems.