INTRODUCTION: Illness and hospitalisation, even of short duration, pose separate risks for permanently reduced functional performance in elderly medical patients. Functional assessment in the acute pathway will ensure early detection of declining performance and form the basis for mobilisation during hospitalisation and subsequent rehabilitation. For optimal results rehabilitation should begin immediately after discharge.The aim of this study is to investigate the effect of a systematic functional assessment in the emergency department (ED) of elderly medical patients with reduced functional performance when combined with immediate postdischarge rehabilitation. METHOD AND ANALYSIS: The study is a two-way factorial randomised clinical trial. Participants will be recruited among patients admitted to the ED who are above 65 years of age with reduced functional performance. Patients will be randomly assigned to one of four groups: (1) functional assessment and immediate rehabilitation; (2) functional assessment and rehabilitation as usual; (3) assessment as usual and immediate rehabilitation; (4) assessment and rehabilitation as usual. PRIMARY OUTCOME: 30 s chair-stand test administered at admission and 3 weeks after discharge. ETHICS AND DISSEMINATION: The study has been approved by the Regional Scientific Ethical Committees of Southern Denmark in February 2014. The study findings will be published in peer-reviewed journals and presented at national and international conferences. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier: NCT02062541.