Purpose <p>To compare the longitudinal development of spherical equivalent refraction (SER) and ocular biometric components in the more hyperopic (MoreH) and less hyperopic (LessH) eyes of children with hyperopic anisometropia.</p> Methods <p>This prospective longitudinal study included 36 children aged 4 to &lt;13 years with hyperopic anisometropia without strabismus. Based on a best-corrected interocular visual acuity difference ≥0.20 logMAR, participants were classified as amblyopic (<i>N</i> = 31) or non-amblyopic (<i>N</i> = 5). SER was derived from cycloplegic refraction and anisometropia was defined as an interocular SER difference ≥1 D. Axial length (AL), anterior chamber depth (ACD), lens thickness (LT), and keratometry (K1, K2) were obtained. Corneal curvature (CR) was calculated and the AL/CR ratio determined. Mean follow-up was 3.7 ± 1.4 years, with 5.8 ± 2.4 visits per child. A linear mixed-effects model estimated the rate of change for SER and the ocular components, comparing the MoreH and LessH eyes.</p> Results <p>Baseline anisometropia was 2.66 ± 1.22 D. There were significant differences between the MoreH and LessH eyes for baseline AL, ACD and AL/CR (all <i>p</i> &lt; 0.05). SER change with age was slower for the MoreH than the LessH eyes (−0.11 vs. −0.31 D/year, <i>p</i> &lt; 0.001). The rates of change for AL (0.11 vs. 0.19 mm/year, <i>p</i> &lt; 0.05) and AL/CR (0.01 vs. 0.02, <i>p</i> &lt; 0.001) also were slower for the MoreH eyes. Anisometropia increased with age in the amblyopic subgroup (0.08 D/year) and decreased in the non-amblyopic subgroup (−0.17/D/year; <i>p</i> &lt; 0.001).</p> Conclusions <p>In children with hyperopic anisometropia, axial elongation was slower in the MoreH than in the LessH eyes, particularly in those with amblyopia.</p>