Background: One in three children and adolescents experience knee pain. Approximately one in two adolescents with knee pain will continue to experience pain even five years later and have low quality of life. The general practitioner (GP) is the first point of contact for children and adolescents with knee pain in Denmark. There is a variety of treatments being delivered in general practice, despite similar symptoms and patients' characteristics. This suggests a need to support the GPs in identifying those at high risk of a poor outcome early on, in order to better allocate resources. The aim of this study is to develop a user-friendly prognostic tool to support GPs' management of children and adolescents' knee pain. Methods: A preliminary set of items in the prognostic tool were identified using systematic reviews and meta-analysis of individual participant data. Following feedback from GPs and children and adolescents on the content and understanding, the tool was piloted and implemented in general practice. A cohort of approximately 300 children and adolescents (age 8-19 years old) is being recruited from general practices (recruitment period, July 2019 - June 2020). Clinically meaningful risk groups (e.g. low/medium/high) for the recurrence/persistence of knee pain (at 3 and 6 months) will be identified. Discussion: If successful, this prognostic tool will allow GPs to gain insights into the likely prognosis of adolescents with knee pain and subsequently provide the first building blocks towards stratified care, where treatments will be matched to the patients' prognostic profile. This has the potential to improve the recovery of children and adolescents from knee pain, to improve the allocation of resources in primary care, and to avoid the decline in physical activity and potential associated health and social consequences due to adolescent knee pain. Registration: Registered with ClinicalTrials.gov on 24 June 2019 (ID NCT03995771).