The present study aimed to analyze and compare gender differences in the basic psychological needs (BPN) in several subjects (Physical Education, Mathematics, English and Language, and Literature) in terms of satisfaction/frustration, the perceived subject importance, and perceived usefulness of the subject matters, and the degree of enjoyment/boredom perceived by secondary students. In addition, the differences between the subjects in the mean scores of all these motivational variables were analyzed. Participants were 1754 Spanish students (986 girls and 768 boys) in 3rd (n = 991) and 4th grade (n = 763) of secondary education with an average age of 15.70 years (± 0.75). An independent-sample t-test to assess possible gender differences and a paired t-test were carried out to compare the variables in the different subjects. The results revealed significant differences in the majority of variables analyzed according to gender, with higher values for girls than boys in need satisfaction, the perceived usefulness the enjoyment of most subjects, and lower values in need frustration and boredom. In addition, significant differences were found when comparing the four subjects. Specifically, Physical Education (PE) had significantly higher values in need satisfaction and enjoyment and significantly lower scores in need frustration, perceived usefulness, and boredom than the other subjects analyzed. These gender and betweensubjects differences should be considered when teachers design and develop methodological strategies to carry out their roles with young students.