We conducted a systematic review and meta-analysis to examine if individuals with reading difficulties (RD), mathematics difficulties (MD), or unspecified learning difficulties (ULD) experience internalizing problems (i.e., anxiety, depression, somatic complaints, and social withdrawal) to the same extent, and if the effect sizes are influenced by moderators (age, internalizing problems type, anxiety type, rater type, selection criteria, and attention control). We reviewed 2,806 studies published in English between January 2000 and April 2023. Our final sample consisted of 96 studies that reported effect sizes or data to calculate them (a total of 120 unique samples, 83,260 participants, age range = 7.3-34.8 years). Risk of bias and sensitivity were assessed. A random-effects model analysis revealed a significant and moderate overall effect size (Hedge's g = -0.54), indicating that individuals with RD, MD or ULD experience more internalizing problems than their chronological-age (CA) controls. Follow-up analyses showed that neither learning difficulties type nor age of participants were significant moderators, but selection criteria (diagnosis versus screening) and internalizing problems type were. These findings suggest that individuals with RD do not differ from those with MD or ULD in internalizing problems, and all fare poorly compared to CA controls.