Intelligent Tutoring Systems are a genre of highly adaptive software providing individualized instruction. The current study was a conceptual replication of a previous randomized control trial that incorporated the intelligent tutoring system Native Numbers, a program designed for early numeracy instruction. As a conceptual replication, we kept the method of instruction, the demographics, the number of kindergarten classrooms (n = 3), and the same numeracy and intrinsic motivation screeners as the original study. We changed the time of year of instruction, changed the control group to a wait-control group, added a maintenance assessment for the first group of participants, and included a mathematical language assessment. Analysis of within- and between-group differences using repeated measures ANOVA indicated gains of numeracy were significant only after using Native Numbers (Partial Eta Square = 0.147). Results of intrinsic motivation and mathematical language were not significant. The effect size of numeracy achievement did not reach that of the original study (Partial Eta Square = 0.622). Here, we compared the two studies, discussed plausible reasons for differences in the magnitude of effect sizes, and provided suggestions for future research.