In earlier investigations, Perilla frutescens (L.) Britt. cv. Chookyoupjaso (CJC) mutants were obtained following mutagenesis induced by 200 Gy of $gamma$-rays. The aim of this study was to compare the CJC and 6 P. frutescens (L.) Britt. cv. Chookyoupjaso mutant lines (CJMs), with respect to their phytochemical profiles and to evaluate anti-inflammatory properties by selecting the most bioactive CJM. The methanol extracts of CJMs were tested for inhibition of nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells. Among them, CJM-45 showed significant inhibition of NO production. This extract was further partitioned using ethyl acetate (EtOAc), butanol (BuOH), and water. The EtOAc fraction (EF-cjm45) was evaluated for antiinflammatory activities. These results indicated that the EF-cjm45 reduced NO production by inhibiting inducible nitric oxide synthase (iNOS) expression. The EF-cjm45 treatment also significantly diminished expression of MCP-1 and IL-6. In the EF-cjm45, perillaketone, isoegomaketone, ursolic acid, kaempferol, and rosmarinic acid were also found. This study reveals the potential therapeutic use of bioactive CJM-45 and justifies the wide application for this plant in traditional medicine.