To compare the subfoveal, parafoveal, and peripapillary choroidal thickness in amblyopic eyes with fellow and control eyes. Twelve control eyes, six fellow eyes, and six amblyopic eyes in this cross-sectional study. Choroidal thickness was measured by the enhanced-depth imaging technique of optical coherence tomography in all subjects. Choroidal thickness was measured at the subfoveal area and at 1000 mm intervals to the nasal and temporal to the fovea up to 2000 mm. The mean age was 8.75 ± 2.73 years in controls and 9.50 ± 2.81 years in amblyopic patients. Parafoveal choroidal thickness was thickest subfoveally, but thinnest nasally, in all three groups. The mean subfoveal choroidal thickness was 256 ± 40 in control eyes, 226±44 in fellow eyes, and 270±34 in amblyopic eyes. It was thicker in amblyopic eyes but not significantly, P-value > 0.05. There was no significant result in choroidal thickness between amblyopic, fellow, and control eyes.