Purpose: Fatigue is a distressing symptom commonly reported among pediatric patients with primary immunodeficiency (PID). However, the relationship between fatigue and disease activity is currently unknown. Methods: In this cross-sectional study, we examined the prevalence of severe fatigue, the effect of fatigue on health-related quality of life (HRQoL), and the effects of disease activity and comorbidity on fatigue severity among pediatric patients 2–18 years of age with PID. Fatigue and HRQoL were assessed using the pediatric quality of life inventory multidimensional fatigue scale (PedsQL MFS) and generic core scales (PedsQL GCS), respectively. Linear regression analyses and an analysis of covariance were used to compare the fatigue scores with the scores obtained from a healthy control group. Data were adjusted for age and sex. Results: Of the 91 eligible patients, 79 were assessed (87% participation rate), with a mean age of 10.4 ± 4.4 years. Pediatric patients with PID reported significantly higher fatigue levels compared to healthy peers, with an 18.9% prevalence of severe fatigue. Moreover, higher fatigue levels were inversely associated with HRQoL in all domains and directly associated with school absences. We found that severe fatigue was comparable between common variable immunodeficiency (CVID), combined immunodeficiency (CID), and selective immunoglobulin A deficiency (SIgAD) patients, but was not reported in the X-linked agammaglobulinemia (XLA) patients studied. Finally, fatigue severity was not significantly associated with disease activity or comorbidity. Conclusions: Nearly 20% of pediatric patients with PID reported experiencing severe fatigue, and fatigue was reported among a wide range of PID subcategories. In addition, severe fatigue negatively affected the patient’s quality of life and daily functioning, but was not associated with disease activity or comorbidity. Thus, targeting severe fatigue might be a promising strategy for improving the overall well-being and quality of life of pediatric patients with PID.