Abstract Background Inflammatory Bowel Disease (IBD) has emerged as a public health challenge. In addition to the health effects on patients, IBD also carries a significant economic impact. The diagnosis, treatment, and follow-up of IBD entail considerable costs for both patients and the healthcare system. Therefore, understanding the economic impact of this disease is crucial for making informed decisions about its management and resource allocation. The aim of this study was to determine the short-term (one month) and long-term (twelve months) economic impact of medical care and surgical treatment in patients diagnosed with IBD at a tertiary-level hospital in Mexico. Methods A retrospective study was conducted, which included 118 patients diagnosed with IBD and treated at the IBD Clinic of the "Dr. Eduardo Liceaga" General Hospital in Mexico over the past 12 months. The economic impact of both medical treatment (conventional and biological) and surgical treatment in managing IBD was evaluated. For the calculation of medical treatment costs, the unit costs of medications were based on maximum retail prices at a conventional pharmacy. Surgical treatment costs were based on the hospital's provided costs. Individual costs for each patient were recorded and tabulated, and the total cost for each treatment regimen was calculated at one and twelve months. Descriptive statistical methods were used to analyze the data to obtain measures of central tendency and dispersion. Results The average monthly cost of medical treatment for a patient with IBD is estimated to be $11,612.45 Mexican pesos (MXN), resulting in a total cost of $139,349.40 MXN over 12 months. Considering all our patients, the total cost of medical care reaches $16,443,229.20 MXN in 12 months. Regarding surgical treatment, there is an average cost of $626,847.45 MXN per surgical event in patients with IBD. The total cost of surgical treatment for our IBD patients, encompassing a total of 24 patients, amounts to $15,043,379 MXN. Therefore, medical treatment appears to be more cost-effective compared to surgical treatment (the total cost of medical treatment for the 121 patients over one year is $16,443,229.20 MXN, while the total cost of surgical treatment for the 24 patients is $15,043,379 MXN). In our institution, 95% of the IBD Clinic patients receive free medical care. This represents significant cost savings for patients. Conclusion This study provides evidence regarding the economic impact of medical and surgical treatment in patients with IBD. The results support the consideration of medical treatment as the more cost-effective option while emphasizing the significance of free medical care in improving equitable access and alleviating the financial burden on patients and their families.