Basic motor skills are the basis for the formation and execution of movements that will be utilized throughout an individual’s lifetime, thus promoting their involvement and continued participation in physical activity. (1) Background: This study aimed to assess the impact of a physical education program, based on a model of structured and unstructured physical activity, on the motor development of kindergarten students at a private school for girls in Con Con, Chile. (2) Methods: Thirty-four female students were divided into two groups, one participated in structured physical activity and the other in unstructured physical activity, and both groups then underwent a 12-week intervention. The Test of Gross Motor Development-2 (TGMD-2) was utilized to evaluate motor behaviors, and the data were analyzed using descriptive statistics and relative frequencies. The Wilcoxon test was used to compare differences at the beginning and end of the intervention, while the Whitney–Mann U test was used to determine differences between groups. (3) Results: Statistically significant differences were observed in the overall group when comparing the start and end of the intervention for total motor development (p = 0.001), locomotion skills (p = 0.018), and object control (p = 0.001). However, no significant differences were found between the two types of intervention activities. (4) Conclusions: This study suggests that both structured and unstructured physical activity interventions enhance overall motor development, particularly in the dimensions of locomotion and object control. The results indicate that unstructured physical activity interventions may lead to better outcomes in motor development tests compared to structured interventions.