Studies have suggested that maternal autoimmune diseases are associated with an increased risk of attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). However, research on the association of paternal autoimmune diseases with ADHD and ASD risk has remained inconclusive. Using the Taiwan National Health Insurance Research Database, we selected 708,517 family triads (father–mother–child) between 2001 and 2008 and followed them until the end of 2011. Parental autoimmune diseases as well as ADHD and ASD in children were identified during the study period. Increased ADHD risk in children in terms of hazard ratios (HRs) and 95% confidence intervals (CIs) was associated with prenatal exposure to paternal autoimmune diseases, including Sjögren’s syndrome (HR: 8.41, 95% CI: 2.72–26.05), psoriasis (HR: 1.95, 95% CI: 1.05–3.63), and ankylosing spondylitis (HR: 2.02, 95% CI: 1.29–2.15), as well as maternal autoimmune diseases, such as systemic lupus erythematosus (HR: 1.53, 95% CI: 1.09–2.15), type 1 diabetes mellitus (HR: 1.55, 95% CI: 1.02–2.36), inflammatory bowel disease (HR: 2.37, 95% CI: 1.59–3.52), psoriasis (HR: 1.70, 95% CI: 1.00–2.87), and ankylosing spondylitis (HR: 2.07, 95% CI: 1.11–3.86). However, ASD was only associated with paternal inflammatory bowel disease (HR: 3.08, 95% CI: 1.15–8.28) and ankylosing spondylitis (HR: 2.65, 95% CI: 1.10–6.39). Both paternal and maternal autoimmune diseases were associated with increased likelihood of ADHD in children. However, only paternal autoimmune diseases were related to offspring ASD risk. The precise pathomechanism underlying the correlation between parental autoimmunity and child neurodevelopment requires further investigation.