Purpose. Our study aimed at assessing the effects of introducing a modified physical educational program that uses “eduball” educational balls during exercise, play-time and games on the physical fitness of first-grade primary school students. In addition, the study also took under consideration whether any noted changes depended on where the students lived, i.e., in an urban or rural environment. Methods. A total of 127 first-grade students were selected to participate in the pedagogical experiment, with 48 students from a primary school in an urban environment and 79 students from two primary schools located in rural villages. The physical fitness levels of the children were assessed by using selected batteries from the International Physical Fitness Test before and after implementing the “eduball” physical education program. Results. The results found that physical fitness levels were not affected by the use of the “eduball” educational ball, regardless of the environment. However, the physical fitness results of both the boys and girls in the rural experimental group may confirm that the activities that used the educational balls, which emphasize running, can have an impact on the motor development of children’s speed and agility skills. Conclusions. The boys from the urban experimental and urban control groups in both tests achieved better results than their peers from rural areas. However, this may be more strongly related to the overall higher physical fitness levels of the boys from an urban environment (as was found in the first test), rather than their place of residence or their schools’ sports facilities, which were found to be comparable. In the groups of girls, a somewhat different trend was observed, with girls from the urban environment performing better than girls from rural areas among the analyzed fitness variables in the first test, but with the differences leveling out by the second test.