Objectives <p>This study aimed to conduct a systematic review on health economic evaluations of fecal microbiota transplantation (FMT) for non-Clostridioides difficile infection (non-CDI) related diseases.</p> Methods <p>A systematic search of literature was conducted up to October 2025 in MEDLINE (Ovid), Embase (Ovid), APA PsycINFO, Web of Science, Scopus, and CINAHL Ultimate. Studies inclusion criteria were: (1) Non-CDI related diseases; (2) FMT as a treatment; (3) health economic evaluations; and (4) original research articles published in English. The quality of included studies was evaluated using the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist.</p> Results <p>Six studies were included. All studies were conducted from the healthcare provider’s perspective, and one additionally considered the societal perspective. Three studies (50%) were cost analyses (<i>n</i> = 1 inflammatory bowel disease (IBD); <i>n</i> = 2 fecal donor screening for treatment of melanoma and metabolic syndrome-associated diseases), two (33%) were cost-effectiveness analyses (IBD), and one (17%) was cost-consequence analyses (urinary tract infection (UTI) caused by multidrug-resistant organisms (MDROs)). The studies were classified as excellent (<i>n</i> = 1), very good (<i>n</i> = 2), and insufficient (<i>n</i> = 3). Four studies (67%) reported that FMT was a potentially cost-saving intervention for IBD (<i>n</i> = 3) and UTI (<i>n</i> = 1). One cost-effectiveness study of 3 FMT regimens for IBD treatment showed the number FMT administrations was influential to total treatment cost.</p> Conclusions <p>The included health economic evaluations of FMT for non-CDI related diseases are scarce and quality is diverse. The small number of analyses highlights the research gap of health economic evaluation of FMT for non-CDI related diseases with positive clinical benefits.</p>