BackgroundPyometra is a common infectious condition, especially in elderly bitches. In addition to an infected uterus, dogs may have concurrent urinary tract infection (UTI). The preferred treatment is surgical removal of the ovaries and uterus, whereupon the general prognosis is excellent. In addition, antimicrobial therapy is frequently prescribed for postoperative treatment. However, no research exists on the benefit of postoperative antimicrobial treatment in uncomplicated canine pyometra. Antimicrobial resistance has become a major challenge in treatment of bacterial infections. Diminishing overuse of antimicrobial agents is essential for controlling the development of antimicrobial resistance in both animals and humans.MethodsThis double-blinded, randomized, placebo-controlled two-arm clinical trial is designed to compare the incidence of postoperative infections associated with surgical treatment of uncomplicated pyometra followed by two different treatment protocols. For the study, 150 dogs presenting with an uncomplicated pyometra and that are to undergo surgical treatment will be recruited. Dogs with body weight < 3 or > 93 kg, complicated pyometra, primary disease increasing the risk of infection, or immunosuppressive medication will be excluded. All dogs will receive one dose of sulfadoxine-trimethoprim intravenously as an antimicrobial prophylaxis. Postoperatively, dogs will be randomized to receive either a five-day course of placebo or an active drug, sulfadiazine-trimethoprim orally. During the surgery microbiological samples will be taken from urine and uterine content. The follow-up includes a control visit in 12 days and an interview of the owner 30 days after surgery. If bacteriuria is detected at the time of surgery, a urinary sample will be cultured for bacterial growth at the control visit. The primary outcome is the incidence of a postoperative surgical site infection (SSI), and the secondary outcome is the occurrence of clinical UTI with bacteriuria. Intention-to-treat and per-protocol analyses will be performed to compare outcome incidences between the treatment groups.DiscussionResearch-based evidence is necessary to create treatment guidelines for judicious use of antimicrobials. The goals of this study are to provide evidence for reducing the use of antimicrobials and targeting the treatment to patients proven to benefit from it. Publishing the trial protocol will increase transparency and promote open science practices.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12917-023-03629-w.