AimHealth workers are the key drivers for strengthening Prevention of Mother-to-Child Transmission (PMTCT) program information management in the health facilities. Thus understanding how health workers perceive information management can enlighten areas that require interventions to improve information management processes in the health facilities. The purpose is to assess health workers' perceptions toward PMTCT program information management and factors affecting information management in the health facilities.MethodsThe study was conducted in five out of forty-three health facilities providing PMTCT services in Lilongwe district and thirty out of sixty-eight health workers were recruited across the study sites. Purposive and convenience sampling were used. Semi-structured questionnaires and in-depth interviews were used to collect demographic information and health workers' perceptions toward information management, respectively. Thematic and content analysis techniques were employed for qualitative data, while descriptive statistics were used for quantitative data.ResultsMost health workers perceived information management tasks as part of their job description, but less important to provision of clinical services. For many, use of information technology tools was viewed as beneficial and valuable, whereas the paper-based system was perceived as tedious and difficult to manage. In addition, some believed lack of feedback, information sharing, and poor attitude toward information management tasks were challenges.ConclusionBased on the study findings, there is need to find ways of motivating data quality improvement practises in the health facilities, as health workers view this as a tangential, non-essential part of their job. Health facility leadership needs to promote an information culture through enforcement of meetings, supervision and provision of feedback. The government and its partners should continue rolling out and enhancing competence of health workers on EMR in the health facilities whilst also addressing challenges mentioned in the study.