Background Pituitary stalk interruption syndrome (PSIS) is rare in the paediatric population. It combines ectopic posterior pituitary stalk interruption and anterior pituitary hypoplasia with hormonal deficiencies. The phenotype is highly heterogeneous and obesity/overweight seems to be underreported in the literature. Objective To identify patients with PSIS and obesity or overweight, describe their phenotype, and compare them with patients with PSIS without overweight/obesity. Methods Sixty-nine children and young adults with PSIS in a Toulouse cohort from 1984 to 2019 were studied. We identified 25 obese or overweight patients (OB-OW group), and 44 were non-obese/overweight (NO group). Then, the groups were compared. Results All cases were sporadic. The sex ratio was 1.6. The main reason for consultation in both groups was growth retardation (61% in OB-OW group, 77% in NO group). History of neonatal hypoglycaemia was more common in OB-OW than in NO group (57% vs. 14%, p = 0.0008), along with extra-pituitary malformations (64% vs. 20%, p < 0001). The incidence of caesarean section was higher in OB-OW group (52%) than in NO group (23%), although not significant (p = 0.07). Conclusion Patients with obesity/overweight and PSIS display interesting phenotypic differences that suggest hypothalamic defects. Studies are needed that include additional information on hormonal levels, particularly regarding oxytocin and ghrelin.