The Lower (YBT-LQ) and Upper (YBT-UQ) Quarter Y Balance Test are well established assessment tools for the examination of dynamic balance and shoulder mobility/stability, respectively. However, investigations on YBT-LQ/UQ performance in students with borderline intellectual functioning (BIF) (i.e., intelligence quotient of 70–84 etc.) are lacking. Thus, the aim of the study was to compare YBT-LQ/UQ performance in students with and without BIF. Thirty students with BIF (age: 13.7 ± 1.2 years) and 30 age-/sex-matched students without BIF (age: 13.7 ± 1.3 years) performed the YBT-LQ and/or YBT-UQ. Normalized maximal reach distances (% leg/arm length) per reach direction and the composite score were used as outcome measures. A univariate analysis of variance was conducted to test for significant group differences. Irrespective of limb and reach direction, students with BIF compared to those without BIF showed significantly worse YBT-LQ ( p ≤ 0.001–0.031; Cohen’s d = 0.57–1.26) and YBT-UQ ( p ≤ 0.001–0.015; Cohen’s d = 0.68–1.52) performance with moderate to large effect sizes. Due to the poorer performance levels of students with BIF, specifically tailored interventions should be developed that have the potential to improve their dynamic balance and shoulder mobility/stability.