The development of children’s fundamental motor skills (FMS) is shaped by the environment surrounding them. The purpose of this study was to examine whether the changes of children’s FMS after an intervention program differed between classes conducted in different schooling conditions. Participants were 295 preschool children (62 boys, 133 girls; M = 5.4 years; SD = 0.28) from eight preschools in Hong Kong. Children participated in an 8-week FMS program and their FMS were assessed using the Test of Gross Motor Development-2 (TGMD-2). A linear mixed model was used to analyze the association on the changes of FMS score between children in different schooling conditions: (1) teaching venue size (large or small); and (2) class size (large, medium, or small), while accounting for the clustering of participants within preschools. The changes of object control skills were significantly different between groups with different teaching venue size (p = 0.000) (small: 5.54 (SD = 5.84) vs. large: 2.46 (SD = 6.42)) and different class size (p = 0.000) (small: 8.12 (SD = 6.34) vs. medium: 2.92 (SD = 6.26) vs. large: 4.00 (SD = 5.79)). The findings have practical implications for the teaching of FMS in that the social and physical environment in preschools should be considered for the design of FMS intervention programs. Copyright © 2020 by the authors. Licensee MDPI, Basel, Switzerland.