The modern teaching/learning environment is, like never before, rich with digital teaching/learning technologies and tools that are becoming part of children’s daily lives. Background: In Lithuania, virtual teaching/learning platforms (environments for mathematics, knowledge of nature, history, and language practice) in primary education became more widely used approximately three years ago after the implementation and application of the virtual teaching/learning platform EDUKA. The purpose of this study was to establish the effect of the virtual teaching/learning platform EDUKA on the learning outcomes of primary-grade students in the subject of mathematics. Methods: In this study, a pre-test/middle-test/post-test experimental strategy was used to avoid any disruption of educational activities due to the random selection of children in each group. Mathematical diagnostic progress tests (MDPTs) are an objective way to measure skills and abilities. The MDPTs were divided into two sections: the tasks were allocated according to performance levels and the content, as well as fields of activity and cognitive skills. The assessment of all areas of activity was based on the primary school children’s performance (i.e., unsatisfactory, satisfactory, basic, and advanced). Results: An analysis of the results of the MDPTs showed that, across the seven possible tasks, both male and female seven-year-old children achieved satisfactory results (results were observed between groups) (post-test: control gathering (CG) 5.10; test gathering (EG) 5.04; p = 0.560), basic results (post-test: CG 6.28; EG 6.42; p = 0.630), and advanced results (post-test: CG 1.90; EG 2.27; p = 0.025). The differences between the pre-test and post-test advanced (p = 0.038) and the pre-test and post-test basic (p = 0.018) levels were found to increase. Conclusions: It was found that intensively integrating the virtual learning platform EDUKA into formal education—specifically in the subject of mathematics—had a significant impact on primary school children’s mathematical performance. In addition, after the experiment, a statistically significant difference was found (p < 0.05) in primary school children with higher levels. The intervention in the experimental group (i.e., integration of the virtual learning platform into the formal mathematics learning process) had a positive impact on access to mathematics. Students’ math learning achievements were positive in progressive mathematics.