Conditions that cause bone dysplasias and premature closure of sutures are rare. This study aims to discuss the underlying condition of a juvenile exhumed from the São Martinho church graveyard, Leiria, Portugal. The necropolis's stratigraphy dates this individual ca. 1211 AD, the date the church was founded. The skeleton is 84% complete, and the bones are well preserved. Pelvic morphology indicates a male individual. Age at death estimated from the length of the third molar was 17.8 years, whereas skeletal maturation indicated an age ranging between 14 and 16 years. The unusual features of this individual include (a) a stocky body with rugose muscle attachment sites, particularly on the clavicle and upper limb bones, and short long bones; (b) squamous and parieto‐mastoid sutures synostosis that resulted in an asymmetrical vault and mandible. Femur length is consistent with 9.5–12.0 years old. Hundreds of conditions can cause short stature. In this individual, the skeletal characteristics point to a mild form of skeletal dysplasia consistent with hypochondroplasia. However, only genetic tests could confirm this hypothesis. Despite his appearance, this individual survived to late adolescence and was buried in the same way as the other individuals of this medieval community. This study reports the first case of skeletal dysplasia in the Portuguese palaeopathological record.