Background: Punctal agenesis (PA) is a rare congenital anomaly that can occur in isolation or as part of an underlying syndrome. The benefit of genetic assessment in individuals with PA and clinical features that should prompt molecular workup has not been systematically studied. The aim of this study was to identify ocular and extraocular features associated with PA and determine its association with an underlying syndrome. Methods: A retrospective medical records review of ocular and extraocular medical histories in all patients diagnosed with PA at the Children’s Hospital of Philadelphia between 2009 and 2023 was conducted. Results: Forty-four patients were included, ages 3.3 ± 3.3 years. Our cohort was 31 males (70%). Twenty patients had isolated PA (45.5%), while 24 patients (54.5%) had other associated ocular or extraocular abnormalities. The most common ocular comorbidities were refractive disorders (n = 8, 33%), ptosis (n = 8, 33%), strabismus (n = 7, 29%), other eyelid disorders (n = 9, 38%), and amblyopia (n = 6, 25%). Nineteen (43%) individuals had systemic disorders and 18 (41%) underwent genetic testing. An associated genetic diagnosis was found in 17 (39%) individuals. The most common associated syndrome was ectodermal dysplasia. Systemic disorders were more prevalent in individuals with syndromic PA (4, 20% isolated PA vs. 15, 63%, PA-plus, p = 0.005). Conclusions: The presence of additional ocular abnormalities was associated with an increased rate of systemic disorders (63%). In individuals with PA who also exhibit additional ocular disorders, systemic evaluation and genetic workup should be considered.