Background: Performing functional magnetic resonance imaging (fMRI) examination is difficult when a child needs to stay awake and cooperate. Many techniques help to prepare them for the study but without modification of the examination protocol. The objective of this research was to prepare a gamified motor paradigm (“computer game”) that will improve the fMRI examination of young children. Methods: After preparing a dedicated application the fMRI examination was performed on 60 healthy children (10 girls and 10 boys in each age group of 4, 5, and 6 years old). Each child performed the gamified and a standard motor paradigm, both based on squeezing a rubber bulb. The effectiveness of squeezing were compared. Results: With the application of the gamified paradigm children completed significantly more active blocks (3.3 ± 1.4) than for the standard paradigm (2.2 ± 1.6) (p < 0.0001). In mixed-effects Poisson regression, age (IRR = 1.9; 95%CI: 1.5–2.5) and application of gamified paradigm (IRR = 5.6; 95%CI: 1.1–28.0) were significantly associated with more completed blocks. Conclusions: The gamified motor paradigm performed better than a standard paradigm in the fMRI examination of children between 4 and 6 years old. It allowed a significant increase in the number of completed active blocks and also better squeezing effectiveness in each block.