In this study, a Porphyromonas gingivalis (P.g.)-infected mouse periodontitis model was used to investigate the effect of omega-3 fatty acid intake on differentiation and maturation of cultured osteoclast. Four-week-old C57BL/6JJcl mice were divided into four groups according to the diets they were fed from the beginning of the experiment (i.e., food containing omega-3 or omega-6 fatty acids) and whether they were orally administered P.g. Thirty-three days after beginning the experiment, bone marrow cells were sampled from the femoral bone of mice from each group and differentiated into osteoclasts; the effects of the ingestion of different fatty acids were subsequently investigated. There was no statistical interaction between the different fatty acids and P.g. infection on the number of osteoclasts (P = 0.6). However, the fatty acid type affected the number of osteoclasts in mice (P = 0.0013), with the omega-3 groups demonstrating lower osteoclast numbers than the omega-6 groups. Furthermore, the addition of resolvin E1 (RvE1), which is an omega-3 fatty acid-derived lipid mediator, suppressed the differentiation of mouse cultured osteoclasts (P < 0.0001). Therefore, the ingestion of omega-3 fatty acids may suppress osteoclast differentiation while inhibiting bone resorption and tissue destruction due to periodontitis.