Objective To determine whether botulinum toxin is effective and safe for the treatment of epiphora, and to compare its utility in functional versus non-functional epiphora using both qualitative and quantitative methods. Materials and Methods Patients were divided into two groups (functional and non-functional epiphora) according to the presence of lacrimal drainage obstruction. All patients were injected with 2.5 units of botulinum toxin into the palpebral lobe of the lacrimal gland, and improvement in epiphora and quality of life were assessed both objectively and subjectively using Schirmer’s I test, indoor and outdoor Munk scores, TEARS score, watery eye quality of life score, and tear meniscus measurements at pre-injection, and 1, 3, and 6 months post-injection. Functional and non-functional epiphora groups were compared. Results Botulinum toxin was injected into 72 lacrimal glands of 65 patients with functional and non-functional epiphora. In both the functional and non-functional epiphora groups, the mean Schirmer’s I test value, indoor and outdoor Munk scores, TEARS score, watery eye quality of life score, tear meniscus height, depth, and area values improved significantly at 1, 3, and 6 months after injection compared with pre-injection values (p < 0.05). There were statistically significant differences in mean Schirmer’s I test, tear meniscus height, depth, and area values between the functional and non-functional epiphora groups at 1, 3, and 6 months after botulinum toxin injection (p < 0.05). In the functional epiphora group, a greater proportion of patients reported improvement than in the non-functional group. All complications were minor and resolved within 2 weeks after the injection. Conclusion Botulinum toxin injection into the lacrimal glands of patients with functional and non-functional epiphora was a simple, effective, and safe treatment. In addition to qualitative methods, quantitative methods, such as tear meniscus measurement, provided direct evidence that symptomatic improvement occurred more in those with functional versus non-functional epiphora after botulinum toxin injection.