Abstract Background Although there are public policies for eradicating congenital syphilis, they do not seem to be a routine in most health services. The objective of this study was to evaluate the management of sexual partners of pregnant women with syphilis in primary health care in northeastern Brazil. Methods This is a qualitative assessment carried out from February to October 2014 in the city of Fortaleza, Ceará, northeastern region of Brazil, through the observation of six primary health care centers and interviews with 21 professionals, six coordinators, nine women diagnosed with syphilis during antenatal care and four sexual partners. The data were submitted to thematic content analysis. Results Important flaws were identified at the primary health centers studied regarding the management of syphilis during pregnancy. Accessing testing and treatment is difficult, and there are no standardized strategies to notify the partner. The responsibility for notifying them is transferred to the women, and counseling does not offer proper guidance nor sufficient emotional support to help them. Conclusion The management of pregnant women and their sexual partners in our region does not comply with global recommendations. Professional qualification, sensitization, and standardization of health professionals’ conduct are necessary. Offering support to health professionals on their clinical practices by means of a supervision process may contribute to the adoption of the recommended guidelines and to the promotion of care based on privacy, respect, confidentiality of information, and awareness of the problems faced by women as a result of syphilis diagnosis.