The purpose of this study was to know if there was a relation between the perceived competency-based learning and measured learning in TIMSS 2015, by a sample of Spanish and German students. To determine if there was any significant statistical relationship (positive or negative) between the perceived learning of competencies and the learning measured in TIMSS 2015, binary logistic regression analysis was performed in a comparative way between both countries. Participants were 878 students, 523 from Spain and 355 from Germany, from third to sixth school year of primary school. The results showed a high relation between the perceived competency-based learning and the measured learning in TIMSS Mathematics and Sciences, by students of both nationalities. According to the perceived competency-based learning results, the Spanish students presented higher scores of perception in the social and citizenship competencies and learning to learn competencies than the German students. However, no significant statistical differences were found in measured learning in both countries. These results could affirm that the perceived learning could be understood as an influential (and not unique) factor in the measured learning and, on the contrary, a tendency that could relate the high values of perceived learning, according to these results, and the increase in academic performance reported in the international evaluation reports.