To compare corneal higher order aberrations (HOAs) in patients with epiphora caused by unilateral primary acquired nasolacrimal duct obstruction (PANDO) and their fellow eyes. A total of 122 eyes of 61 patients with unilateral PANDO were included. Affected eyes were named as group 1 and contralateral eyes as group 2. The Munk score and fluorescein dye disappearance test (FDDT) were assessed. Corneal topographic and HOAs measurements were taken by Sirius topography. There were 47 female and 14 male patients. The mean keratometry was 43.84 ± 1.4 in group 1 and 43.96 ± 1.4 in group 2 (p = 0.73). The mean corneal topographic astigmatism was 0.81 ± 0.7 in group 1 and 0.78 ± 0.5 in group 2 (p = 0.57). The mean coma-like aberration was 0.19 ± 0.2 in group 1 and 0.10 ± 0.1 in group 2 (p = 0.03). The mean spherical-like aberration was 0.16 ± 0.1 in group 1 and 0.11 ± 0.1 in group 2 (p = 0.04). The mean total corneal HOA was 0.30 ± 0.5 in group 1 and 0.23 ± 0.2 in group 2 (p = 0.04). The mean Munk score was 3.47 ± 1.0 in group 1. There was a positive correlation between the Munk score and both coma-like aberration (r = 0.53, p = 0.003) and total corneal HOAs (r = 0.44, p = 0.010). The mean FDDT grade was 2.60 ± 0.1 in group 1. A positive correlation was observed between the FDDT grade and both coma-like aberration (r = 0.48, p = 0.001) and total corneal HOAs (r = 0.33, p = 0.001). Epiphora in patients with PANDO can affect corneal HOAs. As patients' symptoms and tear pooling were increased as corneal HOA levels increased.