Background We recently found fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) patients to be an effective and safe treatment after 3 months. The present follow‐up study investigated the efficacy and safety of FMT at 1 year after treatment. Methods This study included 77 of the 91 IBS patients who had responded to FMT in our previous study. Patients provided a fecal sample and completed five questionnaires to assess their symptoms and quality of life at 1 year after FMT. The dysbiosis index (DI) and fecal bacterial profile were analyzed using a 16S rRNA gene‐based DNA probe hybridization. The levels of fecal short‐chain fatty acids (SCFAs) were determined by gas chromatography. Results There was a persistent response to FMT at 1 year after treatment in 32 (86.5%) and 35 (87.5%) patients who received 30‐g and 60‐g FMT, respectively. In the 30‐g FMT group, 12 (32.4%) and 8 (21.6%) patients showed complete remission at 1 year and 3 months, respectively; the corresponding numbers in the 60‐g FMT group were 18 (45%) and 11 (27.5%), respectively. Abdominal symptoms and the quality of life were improved at 1 year compared with after 3 months. These findings were accompanied by comprehensive changes in the fecal bacterial profile and SCFAs. Conclusions Most of the IBS patients maintained a response at 1 year after FMT. Moreover, the improvements in symptoms and quality of life increased over time. Changes in DI, fecal bacterial profile and SCFAs were more comprehensive at 1 year than after 3 months. www.clinicaltrials.gov (NCT03822299). The study included 77 IBS patients who had responded to FMT 3 months after transplantation. There was a persistent response to FMT at 1 year after treatment in 86.5% and 87.5% patients who received 30‐g and 60‐g FMT, respectively. In addition, the complete remission rates increased. More comprehensive changes than those found after 3 months were observed regarding fecal bacterial profile and short chain fatty acids.