Pain is a significant problem in stable chronic obstructive pulmonary disease (COPD) and is associated with other symptoms, worse health status and lower functional status. Not much is known about pain in unstable disease. The primary aim of the present study is to investigate prevalence, characteristics and relationships of pain in patients with COPD hospitalized for an acute exacerbation (AECOPD) and indicated for post-acute pulmonary rehabilitation (PR). This cross-sectional observational study included 149 patients (mean age 70.8 (±7.9) years, 49% male, mean forced expiratory volume in one second as percentage of predicted value 35.3 (±12.6)). Pain was assessed using the brief pain inventory. Functional status and health status were measured using the six-minute walking test (6MWT), the Barthel index (BI) and the clinical COPD questionnaire (CCQ), respectively. Pain was prevalent in 39.6% of all patients. Symptom burden was high, especially in patients with pain. Although we found no difference in objective measurements of functional status (6MWT, BI), patients with pain had clinically relevant lower health status (CCQ), attributed to the functional domain. Pain in patients hospitalized for AECOPD and indicated for post-acute PR is a relevant problem and needs more attention. Incorporation of standard pain assessment during exacerbations and post-acute PR is recommended.