Blood pressure (BP), especially systolic BP (SBP), is higher in adult growth hormone deficiency (AGHD) patients than in normal controls. Additionally, obesity is a known risk factor for hypertension, and growth hormone deficiency (GHD) is an important cause of short stature. For children with GHD, attention has been directed solely towards height. Few studies have assessed its potential impact on BP. Here, we investigated the effect of body mass index standard deviation score (BMISDS) on BP in children with short stature. This study included 736 children with short stature divided into two groups based on peak growth hormone (GH) level in GH provocation tests [severe GHD (SGHD) group = 212 children; non-SGHD group = 524 children]. We found that SBP was significantly higher in the SGHD group than in the non-SGHD group (p = 0.045). Additionally, there was a significant positive association between BMISDS and SBP in the SGHD group (β = 3.12, 95% CI: 1.40-4.84, p < 0.001), but no association between these variables was observed in the non-SGHD group. Thus, SGHD patients had a higher SBP than non-SGHD patients. BMISDS is a significant factor for higher SBP in SGHD patients but not in non-SGHD patients.