[Purpose] Prognosis for ametropic amblyopia with astigmatism and the factors influencing the prognosis were examined. [Subjects and Methods] Subjects were 39 eyes of 24 children under 9 years of age who were diagnosed with ametropic amblyopia and astigmatism over 2.00 D at Hyogo College Medicine Hospital between 2003 and 2011. The subjects were divided into three groups, the hyperopic astigmatism group (the hyperopic group), the mixed astigmatism group (the mixed group), and the myopic astigmatism group (the myopic group). To examine the effect of astigmatism, a group with a spherical equivalent of <±2.00 D (the weak refraction group) was also selected. Prognoses for their visual acuity and binocularity, and treatment period were examined. The factors influencing the prognoses were the initial age, visual acuity, spherical equivalent, and astigmatism when the therapy was started.[Results] Visual acuity of 20/20 and binocularity of < 100 seconds by the Titmus Stereo Test (TST) were achieved in all the subjects. Only in the hyperopic group, the subjects with good initial visual acuity had significantly good results of the TST. The treatment period correlated with the initial visual acuity but not with the initial age. The treatment periods were significantly extended in the subjects with poor initial visual acuity in the mixed and weak refraction groups, in the subjects with severe hyperopia in the hyperopic group, and in the subjects with severe astigmatism in the weak refraction group. Moreover, in the hyperopic group, a significant difference in the treatment period was seen between the subjects with the initial visual acuity of > 20/40 and < 20/40. The subjects with the initial visual acuity of < 20/40 had significantly longer treatment periods. [Conclusion] Prognosis for ametropic amblyopia with astigmatism is good. Hyperopia affects the treatment period and prognosis for binocularity. Since astigmatism could prolong treatment period, in patients with severe astigmatism, spectacles should be used as early as possible after diagnosis regardless of normal spherical equivalent.