Anal squamous cell carcinoma (ASCC) is rare, accounting for only 1% of gastrointestinal malignancies. We sought to better understand management strategies for ASCC in the setting of Crohn's disease (CD). A retrospective chart review from 2001 to 2016 was conducted using ICD-9/10 codes for CD (555.9/K50) and ASCC (154.3/C44.520). Adult patients with a diagnosis of CD at the time of ASCC diagnosis were included. Seven patients (five female) were included with a median age of 50 years. The majority presented with perianal pain (three) and bleeding (four). Mean duration of CD was 20 years. Five patients had active perianal fistulizing disease at the time of ASCC diagnosis. Clinical stage at diagnosis of ASCC was stage 0 (n = 1), stage I (n = 1), stage II (n = 1), stage III (n = 2), stage IV (n = 1), and unknown (n = 1). All patients were treated with radiation and chemotherapy. Three patients experienced complications during radiation therapy: fistulizing disease, stenotic disease, and flap necrosis. Two patients had persistent disease at 6 months; one patient underwent abdominoperineal resection (APR) and the other chemotherapy and radiation. Two patients developed locally residual and metastatic disease and died within 1 year of diagnosis. Five-year disease-free survival was 56%. While the standard Nigro protocol remains standard of care in patients with ASCC, in the setting of CD, patients may be best approached as a case-by-case basis and may even require an operation first due to complications from radiation and aggressive nature of disease. Due to poor treatment outcomes, surveillance guidelines for this patient population are necessary.