A clinically significant 47.5-kilobase deletion in the pseudoautosomal region 1 (PAR1), downstream of the SHOX gene, was identified in a 13-year-old female with proportionate postnatal short stature and markedly reduced growth velocity, supporting a diagnosis of SHOX-related short stature. This finding, previously associated with Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS), supports a likely diagnosis of LWD in the absence of overt Madelung deformity. Initiation of recombinant human growth hormone (rhGH) therapy led to a marked improvement in growth velocity. This case underscores the importance of considering enhancer region deletions in the diagnostic work-up of idiopathic short stature, even when clinical features are subtle or atypical.