This institutional case control study was carried out to compare choroidal vascularity (CV) in amblyopic eyes, fellow eyes, and control eyes in children with unilateral hyperopic amblyopia. Sixty-four eyes of 32 childeren with unilateral anisometropic hyperopic amblyopia and 38 eyes of 19 healthy children (controls), aged 3 to 16 years. Subfoveal choroidal thickness (CT) and CV were measured using spectral domain optical coherence tomography. The mean subfoveal CT of amblyopic eyes (338.9 ± 60.0 μm) was greater than that of fellow eyes (315.3 ± 63.3 μm, P = 0.043) and control eyes (313.0 ± 42.1 μm, P = 0.025). The mean CV of amblyopic eyes (0.715 ± 0.020) was greater than that of control eyes (0.700 ± 0.020, P < 0.001). While a positive correlation between CT and CV was found in normal eyes (r = 0.470, P = 0.004), a strong negative correlation existed in amblyopic eyes (r = -0.684, P < 0.001). In conclusion, although mean CV was higher in amblyopic eyes, the negative correlation between CT and CV may suggests insufficient blood supply to the outer retina and choroid in the affected eyes of patients with unilateral anisometropic hyperopic amblyopia.