Understanding the perception that students have about their own cognitive processes is a key aspect that allows for a deeper assimilation of the different factors that affect school performance. However, there is limited evidence explaining the link between students’ perception of their own cognitive functions and their academic performance. The objective of this study was to analyze the association between perception of cognitive functions, such as memory, processing speed, attention, execution of complex tasks and nervousness, and academic performance in Chilean schoolchildren from the province of Biobio. A cross-sectional analytic design was conducted. The sample consisted of 590 elementary school students (12 ± 1.3 years old; 48.3% female) from Chilean public schools. The academic performance was measured by means of the accumulated final grades in the language, mathematics, physical education and health subjects, and the grade point average (GPA) of each student. Moreover, a survey to measure the cognitive functions of the participants was applied. The results show that 20.3% of the students perceived themselves as very nervous and 16.8% felt distracted. Differences in marks were observed in all the measured subjects, as well as in GPAs, depending on the perception of cognitive functions. Thus, the students with low to moderate perceptions of their cognitive functions received lower marks than those who reported a high perception. These results were consistent after a multivariate analysis adjusted for a socio-educational variables model. In conclusion, one in five public school students in the Biobío Region of Chile expressed a low perception of their cognitive functions, which is consistent with their weaker school performance. Therefore, it is believed that integrating curricular activity and cognitive work could potentially boost the perception of said functions, and thus reduce the risk of poor academic performance.