The term health literacy (HL) comprises the handling of health information and disease-specific and generic self-management skills, especially relevant for patients with chronic conditions. Health care professionals (HCPs) should correctly identify patients’ communication needs and their HL levels. Therefore, the aims of the study were (1) to determine inpatient medical rehabilitation patients’ HL based on self-assessment, (2) to evaluate changes from admission to discharge, (3) to identify HCPs estimation of patients’ HL, and (4) to compare the estimated patient HL by patients and HCPs. A combined cross-sectional and longitudinal study was conducted in an orthopedic rehabilitation center in Germany. The multidimensional Health Literacy Questionnaire (HLQ) was filled in by patients (admission, discharge). An adapted version was administered to HCPs (n = 32) in order to assess HL of individual patients. Data from 287 patients were used for the longitudinal analysis, and comparison was based on n = 278 cases with at least two HL estimations. The results showed a significant increase in HL in five of nine scales with small effect sizes. Moreover, HCPs mostly provided higher scores than patients, and agreement was poor to fair. Differences between the HL estimation might lead to communication problems, and communication training could be useful.