BACKGROUND Gastrointestinal microbiome modulation is reported to be an effective therapy to reduce the clinical signs of canine atopic dermatitis (cAD). The killed strain of Enterococcus faecalis FK-23 has been shown to reduce allergic responses in mice and people. OBJECTIVE The aim of this multicentre, double-blinded, placebo-controlled study was to evaluate the safety and efficacy of an orally administered heat-killed E. faecalis FK-23 preparation (FK-23p) for the control of cAD. METHODS Thirty-nine client-owned dogs with clinical signs of nonseasonal cAD were enrolled by 10 veterinarians at 15 hospitals. METHODS Dogs were randomized to either FK-23p at a dose of ≥100 mg/kg/day or placebo. Owner-assessed pruritus Visual Analog Scale (pVAS), clinician-assessed Canine Atopic Dermatitis Extent and Severity Index, 4th iteration (CADESI-4) and daily medication scoring (DMS) were evaluated on days 0, 28, 56 and 84. Owners and clinicians were interviewed about the overall response to treatment (RTT), after the study. RESULTS The CADESI-4 significantly decreased in the FK-23p group compared to the placebo group, by Day 84 (P = 0.035; Wilcoxon-Mann-Whitney U-test). There was no significant difference in pVAS and DMS between the groups. Owners and clinicians reported significantly better RTT in the FK-23p group than the placebo group (P = 0.043 and 0.002, respectively; Wilcoxon-Mann-Whitney U-test). There were no adverse events associated with FK-23p. CONCLUSIONS Oral administration of FK-23p provided a small, but measurable benefit when used as an adjunct treatment, in reducing clinical signs of atopic dogs.