This study assessed the effects of probiotics in canine atopic dermatitis (AD). We enrolled 11 client-owned dogs with AD and randomly allocated them to two groups. The probiotics group (n = 7) was prescribed with Bifidobacterium longum while the control group (n = 4) received a placebo powder once a day for 12 weeks. In both groups, the degree of skin lesions was evaluated based on the Canine Atopic Dermatitis Extent and Severity Index (CADESI)-4. We also measured the transepidermal water loss (TEWL). We assessed pruritus severity using the pruritus visual analog scale (PVAS). Alteration of consumed drug doses was converted into medication scores. All the evaluation indices were surveyed every 4 weeks. In the probiotics group, there was a significant decrease in the CADESI-4 score at 4, 8, and 12 weeks compared to that of the baseline score (p < 0.05). There was no significant difference in TEWL, PVAS, and medication score at each time point and between groups. Although these results showed that Bifidobacterium longum did not reduce pruritus, TEWL, and the dosage of drugs for canine AD, it was effective in improving skin lesions, therefore, probiotics could be considered in canine AD with severe skin symptoms.