Introduction: Congenital syphilis is a major public health problem, and early diagnosis and treatment are necessary to prevent it. Penicillin G benzathine is the treatment of choice in pregnant women; however, it may fail to prevent fetal infection, as in the present case. Case presentation: Male newborn, son of an HIV negative mother with gestational syphilis (venereal disease research laboratory (VDRL) 1:4 dilution, positive treponemal test) diagnosed at week 21 of gestation and treated with three doses of 2 400 000 IU of penicillin G benzathine. At delivery, the mother presented VDRL 1:1 dilution. The newborn was diagnosed with congenital syphilis due to VDRL 1:4 dilution, positive treponemal test, elevated aspartate aminotransferases, hyposthenuria, proteinuria, hematuria, and leukocyturia that resolved after treatment with crystalline penicillin for 10 days. The molecular testing in blood showed a high treponemal load. The VDRL test at 3 months was non-reactive. Conclusions: Preventing congenital syphilis with the recommended treatment for gestational syphilis may fail. Moreover, diagnosing this condition in an asymptomatic newborn is difficult. Therefore, clinical and serological tests are recommended to confirm whether maternal treatment was effective in the fetus.