It is well-established that general anxiety associates with the lower use of adaptive emotion regulation and the higher use of maladaptive emotion regulation. However, no study has previously investigated the impact of cognitive emotion regulation on academic anxieties. Using a sample of secondary school students (N = 391), this study examined the impact of cognitive emotion regulation on math and science anxieties. Math anxiety showed stronger correlations with adaptive than maladaptive emotion regulation, whereas general anxiety showed stronger correlations with maladaptive than adaptive emotion regulation. Hierarchical regression analyses showed that math anxiety was associated with the high uses of acceptance, rumination and other-blame and the low uses of positive reappraisal and putting into perspective. However, with controlling science and general anxieties, math anxiety was associated with the high use of rumination and the low use of positive reappraisal. In contrast, science anxiety was associated with the high uses of acceptance and other-blame and the low use of positive reappraisal. Importantly, however, with controlling math and general anxieties, those science anxiety associations did not remain. Accordingly, these results might provide important insights for the specificity, etiology, and intervention of math anxiety.