Objectives: The Active Early Learning intervention was designed to support childcare educators to imbed physical literacy promoting activities into the daily childcare curriculum. The objective of this study was to determine whether this physical literacy intervention had any influence on motor skill development. Design: 22-week stratified cluster randomised controlled trial. Methods: Fifteen childcare centres (8 intervention, 7 control centres; 314 children, 180 boys, 4.3y ± 0.4) participated in the study. Six motor skills were assessed: object control (ball drop/catch and bean bag throw accuracy), locomotor control (10 m shuttle run), stability (one-leg balance and tiptoe walking on a line), and fine motor control (coin manipulation). Intervention effects were evaluated using linear mixed models adjusted for age, sex, socio-economic status, and centre clustering. Results: There was evidence for an intervention effect on fine motor control (−0.47 s, CI [−0.93 to −0.02], p = .041) and the ball drop/catch task (0.68, CI [0.01–1.35], p = .046), but not for locomotor control, stability, or throw accuracy. Conclusions: Improvements in children's gross and fine motor skills can be achieved with a physical literacy intervention delivered by childcare educators. However, broad enhancement of motor skills cannot be assumed by simply introducing more physical literacy promoting activities into the daily routine, and specific motor skill instruction seems warranted in childcare settings.