To evaluate the level of stereopsis and fusion in patients with anisometropia according to the presence of amblyopia. We included 107 children with anisometropia, divided into groups with non-amblyopic anisometropia (NA, n = 72) and amblyopic anisometropia (AA, n = 35). Normal subjects without anisometropia were enrolled in the control group (n = 73). Main outcome measures were the level of stereopsis and sensory fusion as evaluated by Titmus stereotest and Worth 4-dot test, respectively, using anisometropic glasses. The degree of anisometropia in the NA, AA, and control groups was 2.54 diopters (D), 4.29 D, and 0.30 D, respectively (P = 0.014). Stereopsis (arcsec) was significantly worse in the AA group than the NA and control groups (641.71, 76.25, 54.52, respectively, P < 0.001), while no significant difference was found between the NA and control groups. The rate of fusion was significantly lower in the AA than the NA group (14.3% vs. 65.3%, P < 0.001), and was significantly lower in the NA than the control group (65.3% vs. 80.6%, P = 0.001). The levels of stereopsis and sensory fusion with anisometropic glasses were significantly worse in the AA than in the NA group. The level of stereopsis in the NA group, however, did not differ significantly from that in the isometropic control, while the rate of fusion was significantly lower. Early prescription of anisometropic glasses is needed to improve visual acuity and binocularity in children with possible amblyopic anisometropia.