In Japan, the increase in congenital syphilis (CS) notifications has become a public health concern. We conducted a case series study to describe the characteristics of CS patients and their mothers. Of the 13 mothers who consented to participate, seven had regular prenatal care visits, including four who had tested negative at their first trimester syphilis screening. Only three mothers noted that their partners were tested, with all three partners being diagnosed with syphilis. Raising awareness for syphilis prevention during pregnancy, partner testing, and considering additional syphilis testing at the third trimester of pregnancy during times of increased syphilis prevalence is imperative.