Introduction The aim of this research is to investigate young cancer patients' cognitive functioning and the underlying neurobiological mechanisms when cognitive functions are impaired. The MyBrain protocol is a multidisciplinary study that investigates cancer-related cognitive impairment in children, adolescents and young adults, combining neuropsychology, cognitive neuroscience and cellular neuroscience. The study is exploratory with a wide focus on trajectories of cognitive functions from diagnosis to the end of treatment and into survivorship. Methods and analysis Prospective longitudinal study including patients diagnosed with non-brain cancers at age 7-29 years. Each patient is paired with a control matched on age and social circle. Primary objective Evaluation of neurocognitive function over time. Secondary objectives Evaluation of self-perceived quality of life and fatigue, P300 in an electroencephalography (EEG) oddball paradigm, power spectrum in resting state EEG, serum and cerebrospinal fluid levels of biomarkers of neuronal damage, neuroplasticity, proinflammatory and anti-inflammatory markers and their association with cognitive function. Ethics and dissemination The study is approved by the Regional Ethics Committee for the Capital Region of Denmark (no. H-21028495), and the Danish Data Protection Agency (no. P-2021-473). Results are expected to guide future interventions to prevent brain damage and support patients with cognitive difficulties. Trial registration number The article is registered at clinicaltrials.gov NCT05840575 (https://clinicaltrials.gov/ct2/show/NCT05840575)