The prevalence of stroke increases each year and while mortality from stroke has decreased, the prevalence of comorbidities such as anxiety, depression and fatigue affects as many as 75% of stroke survivors. The aetiology of post-stroke fatigue is not clear, although it has been shown to be interrelated with comorbidities such as stress and depression. Due to the interconnected nature of these comorbidities, it is important to improve the specificity of diagnosis and identify novel therapeutic targets to improve the quality of life for stroke survivors. The investigation of molecular biomarkers associated with post-stroke stress, fatigue, and depression may shed light on the relationships between comorbidities and also contribute to the development of novel diagnostics and therapies. Several biomarkers have been identified for stress, depression, and fatigue, some of which are specific to stroke survivors. However, there remain several gaps in understanding, particularly in relation to the physiological mechanisms underlying these side effects and molecular biomarkers associated with post-stroke fatigue. The aim of this scoping review protocol is to outline the methodologies that will be used to provide a comprehensive understanding of the current literature on biomarkers associated with post-stroke fatigue, stress, and depression, informing future research questions.