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Background: The study explores the association between pain and functional impairment in patients with partially remitted MDD, considering both clinician and patient reported outcomes. Methods: Multicenter, observational, and cross-sectional study, with 583 outpatients with partially remitted MDD. Measures of pain intensity (VAS), functional impairment (SOFAS), depressive symptomatology (HAM-D6), and remission from MDD and functional status from a patient-centered perspective (RDQ) were collected. VAS scores (cut-off: 30) were used to divide the sample in two groups: no pain (n = 274) and pain (n = 309). Descriptive data, correlation and regression analyses were obtained. Results: Functional impairment (SOFAS) and pain (VAS) were negatively and significantly correlated in the total sample, and in the group with pain. Lower pain predicted higher functioning. The pain sub-sample was older, less educated, with higher medical comorbidities, higher HAM-D6 scores, and lower functionality (SOFAS). In the RDQ, the pain group showed significantly higher scores in the symptom-related subscales, and lower scores in the subscales related to positive mental health, functioning and wellbeing. Limitations: Correlational and observational design. The criteria and instruments used to measure pain and to define a threshold might limit the generalizability of findings. Conclusions: Pain and functionality should be assessed and treated in patients with MDD in partial remission. Our results indicate that functionality should be assessed with a broader perspective, that also considers positive mental health features.