Background: Physical fitness in youth is a predictor of health in adulthood. The main objective of the present study was to understand if an enriched sport activity program could increase physical fitness in a population of schoolchildren. Methods: In a sample of 672 children aged 10.0 ± 1.90 years, different motor skills were tested by the 1 kg and 3 kg ball throw (BT), the standing broad jump (SBJ), the 30 m sprint (30mS), the leger shuttle run (LSR), the illinois agility test (IGT), and the quadruped test (QT). Within the controlled-trial, the intervention group (ESA) underwent an additional warm-up protocol, which included cognitive enhancing elements, for 14 weeks while the control group continued with ordinary exercise activity. Results: A significant increase was present regarding the 1 kg and 3 kg BT, the SBJ, the 30mS, and the IGT, while no significant difference was shown regarding the QT and the LSR in the ESA group between pre and post intervention. In the control group, no differences were present for any test except for the QT and the LSR post-test. Conclusion: A 14-week structured physical intervention had moderate effects regarding throwing, jumping, sprinting, and agility in a sample of schoolchildren.