The aim of the present study was to investigate the long-term survival and postoperative complications in horses that had undergone small intestinal resection and a modified anastomosis technique using a partially stapled, functional end-to-end anastomosis. Observational retrospective case series. A total of 25 horses underwent small intestinal resection and a partially stapled, functional end-to-end anastomosis. A modified technique to create a partially stapled, functional end-to-end anastomosis is described. The clinical case records of all horses that fulfilled the criteria between January 1, 2010 and January 1, 2020 were reviewed. Data on short-term survival and postoperative complications were collated. A telephone questionnaire of owners was undertaken to evaluate long-term survival. Duration of follow up was from one to 4232 days (median 785 days). A total of 21/25 (84%) of horses survived to discharge, 19/25 (76%) horses were alive at 6 and 12 months and 64% survived to 2 years. A total of 64% of horses developed at least one postoperative complication. Two horses developed a small intestinal volvulus necessitating repeat laparotomy. One horse had kinking at the anastomosis site diagnosed at post-mortem examination. Partially stapled functional end-to-end anastomosis technique in this study had similar short- and long-term survival to those reported in previous studies using handsewn techniques, but severe complications at the anastomosis site occurred in >10% of cases. The anastomosis technique described appears to have similar short- and long-term survival and complication rates, compared to more commonly used anastomosis techniques. However, there is potential for severe complications at the anastomosis site.