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Abstract Background Neurodevelopmental disorders (NDDs) are a group of conditions that include attention-deficit/hyperactivity disorders, specific learning disorders, autism spectrum disorder, intellectual disability, and other disorders. Raising a child with an NDD can be difficult because it affects the social lives of the parents and their relationships. It also requires the parents to develop another set of skills to deal with their child. These factors increase their risk of depression and anxiety. Aim To measure the prevalence rates of depression and anxiety among parents of children with different NDDs, compare the rates between mothers and fathers, and measure the relevant associated factors. Methodology This study was a prospective, qualitative, cross-sectional, anonymous questionnaire-based study. The participants were 416 parents of children with NDDs in Saudi Arabia. The sample size was determined using the Richard Geiger equation with a 5% margin of error, a 95% confidence level, and a 50% response distribution. The screening was performed using a validated Arabic version of the Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7). These are short and understandable screening tools that assist in identifying and grading the severity of depression and anxiety symptoms. The participants were reached by distributing the questionnaire to parents who followed up with Saudi NDD-related associations, clinics, and psychiatric clinics from November 20 to May 8, 2022. The data were collected, reviewed, and then entered into SPSS 21. Results In total, 416 parents of children with NDDs in Saudi Arabia participated in the study. We demonstrated that 85.1% of parents of children with NDDs had depression and that 85.8% had anxiety. Mothers and fathers had similar rates of depression and anxiety. No significant difference was found between the type of NDD and rates of depression and anxiety in parents. Conclusion Children with NDDs affect their parents’ mental health in terms of increased rates of depression and anxiety. This increase is not correlated with a specific etiology. Healthcare professionals who care for children with NDDs should also assess parental mental health and seek an early diagnosis of mental illness to ensure that the appropriate interventions are provided for parents.