Students with sex chromosome aneuploidies (SCAs) are at increased risk for learning disabilities and often require individualized supports in the school setting. This international survey study used qualitative methods and a bioecological systems framework to inductively capture parent perspectives on the challenges that occur in students with SCAs leading to the need for educational supports, how schools serve children with SCAs, and the types of educational supports that are most helpful. Analysis of parent responses emphasized that challenges with reading, executive function, reduced stamina, social skills deficits, and emotional dysregulation act as barriers to learning, and are frequently triggered by busy or noisy classroom environments led by educators unfamiliar with needs of students with SCAs. Further, skills hovering in the borderline range are common to the SCA phenotype, and are not often well served special education systems challenged by limited resources and strict cut-offs for qualification. Parents report the need to strongly advocate for their child to receive adequate school support services. We recommend developing robust family-school partnerships, increased collaboration between the school and the child’s medical team, and acknowledgement of the significant role the genetic condition plays in the educational experiences of students with SCAs. Specific suggestions for school support plans for students with SCAs are provided.