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Background: School health policies and strategies, ensure a holistic healthy environment for children to harness an effective education. Beside provision of services, a health promoting school (HPS) includes an environment in which children and their parents are active participants and not only recipients. Aim: The study aims at exploring the views of primary and secondary schools children aged 10-17 years, and their parents on future strategic priorities for HPS interventions for the years 2016-20. Methods: The study was a descriptive cross-sectional school-based, conducted in 10 localities (districts) of five purposively selected States in Sudan. Qualitative data was collected by interviewing students and parents using guided focus group discussions and was analyzed using Conceptual Content Analysis Technique. Results: Results were generated from FGDs with 271 students and 191 parents. Training of students, parents and teachers on health issues and first aid, improving health, nutrition and psychosocial services along with physical education were the top five priorities suggested by students and parents. Parents added establishing better coordination mechanisms between schools and families and charity funding for poor families as pressing priorities. Conclusion: The outcomes of priority setting by children and parents through an extensive process of engagement and consultation help in fixing the top priorities in view of constrained resources, therefore attracts political support and facilitate acceptance and endorsement by different levels of decision making.