The aim of this pilot study was to examine the immediate and long-term effects of an intervention program that aims to improve preschoolers’ (N = 36, M = 4.49 years, SD = 0.35) early numeracy skills by combining the learning of numerical relational skills via story reading with fundamental motor skill practice. The intervention program was piloted with two study designs: a within-subject repeated-measures design with 18 children (study I), and a quasi-experimental study design with 18 children (study II). Children’s early numeracy, symbolic magnitude processing, and fundamental motor skills were measured. Results demonstrated that children’s early numeracy and especially numerical relational skills improved during the intervention, and the intervention had larger effects on children’s early numeracy and numerical relational skills compared to the control period (study I) and control group (study II). Furthermore, the results from the delayed post-test demonstrated that the effects were maintained for 4.5–8 weeks after the intervention. These findings provide preliminary evidence that it is possible to support children’s early numeracy skills with combined learning of numerical relational skills via story reading and fundamental motor skills despite the socioeconomic or language background, and narrow the gap between low- and average-performing children.