It is common knowledge that physical exercise is an important factor for a healthy lifestyle. It is important to understand what motivates young people to exercise and what is the difference between different age groups regarding exercise so that we can create tools for further physical activity. The aim of our paper would be to confirm differences and motivation tied to exercise between high school students of different ages. Our test sample involved 147 pupils (male and female) from the 1st and 4th classes off “Civil Engineering and Geodesy Technical School” and “Design, Graphics and Sustainable Civil Engineering School”, 74 students were from the 1st class and 73 students from the 4th class. Variables, shown through 14 factors: weight management, health avoidance, revitalization, appearance, social recognition, stress management, health, strength and endurance, enjoyment, affiliation, health pressures, competing, nimbleness and challenge. The results show significant discrepancies from common findings so in order to confirm the differences we used the Kruskal–Wallis Test. Our conclusion demonstrated that there were significant differences between younger and older students tied to six motivational factors regarding physical exercise. The most significant differences were attached to health avoidance and revitalization favoured by older high school students. We can assume that older high school students have a higher level of responsibility towards their health than their younger colleagues. The final four significant factors (stress management, health, strength and endurance, nimbleness) also show a difference between older and younger students, which again favour the older group so we can confirm that younger students need to be more conscious of the importance of physical exercise for improved health. We can again assume that younger generation does not view physical health as a priority because they are preoccupied with social and other activities that are not tied to physical activity.