We investigated whether gender differences in grades can be attributed to boys being perceived as less competent in self-regulating their own learning by their teachers. N = 1533 girls and boys from 78 fourth grade classes in German primary schools completed standardized performance tests in German reading comprehension and mathematics. Moreover, their teachers provided students’ mid-term grades for German and Mathematics and rated each student’s ability for self-regulated learning. After controlling for test performance in reading comprehension, girls were graded more favorably in German than boys. This difference could partly be explained by their higher competence in self-regulated learning. In mathematics no gender differences in grading or test scores emerged. However, when controlling for teachers’ perception of their students’ ability for self-regulated learning, boys obtained even better grades than girls. We discuss if these results are due to girls being more competent self-regulated learners or to gender stereotypes impacting teachers’ perceptions of their students.