Youth with conduct problems have poorer academic outcomes than their typically developing peers. The objective of the current study was to examine how sexual minority status was associated with trajectories of teacher-rated mathematics and language arts (i.e., reading and writing) achievement in seven consecutive years across the transition to adolescence among youth with childhood histories of conduct problems (N = 383). Sexual minority status (as assessed via indicators of identity, attraction, or behavior during adolescence in the eighth year of the study) was not associated with initial mathematics or language arts performance at time 1, but was associated with declining mathematics achievement during the transition to adolescence. These findings suggest that sexual minority status is linked to change in some aspects academic achievement among youth already at risk for poorer academic achievement (i.e., youth with conduct problems).