Abstract Context Patients with craniopharyngioma suffer from obesity and impaired bone health. Little is known about longitudinal changes in body composition and bone mineral density (BMD). Objective To describe body composition and BMD (change). Design Retrospective longitudinal study. Setting Two Dutch/Swedish referral centers. Patients Patients with craniopharyngioma (n = 112) with a dual X-ray absorptiometry (DXA) scan available (2 DXA scans, n = 86; median Δtime 10.0 years; range 0.4-23.3) at age ≥ 18 years (58 [52%] male, 50 [45%] childhood onset). Main outcome measures Longitudinal changes of body composition and BMD, and associated factors of ΔZ-score (sex and age standardized). Results BMI (from 28.8 ± 4.9 to 31.2 ± 5.1 kg/m2, P < .001), fat mass index (FMI) (from 10.5 ± 3.6 to 11.9 ± 3.8 kg/m2, P = .001), and fat free mass index (FFMI) (from 18.3 ± 3.2 to 19.1 ± 3.2 kg/m2, P < .001) were high at baseline and increased. Fat percentage and Z-scores of body composition did not increase, except for FFMI Z-scores (from 0.26 ± 1.62 to 1.06 ± 2.22, P < .001). Z-scores of total body, L2-L4, femur neck increased (mean difference 0.61 ± 1.12, P < .001; 0.74 ± 1.73, P < .001; 0.51 ± 1.85, P = .02). Linear regression models for ΔZ-score were positively associated with growth hormone replacement therapy (GHRT) (femur neck: beta 1.45 [95% CI 0.51–2.39]); and negatively with radiotherapy (femur neck: beta –0.79 [–1.49 to –0.09]), glucocorticoid dose (total body: beta –0.06 [–0.09 to –0.02]), and medication to improve BMD (L2-L4: beta –1.06 [–1.84 to –0.28]). Conclusions Z-scores of BMI, fat percentage, and FMI remained stable in patients with craniopharyngioma over time, while Z-scores of FFMI and BMD increased. Higher glucocorticoid dose and radiotherapy were associated with BMD loss and GHRT with increase.