Purpose Understanding the integration of pharmacovigilance activities in the healthcare system and identifying existing hindering factors systematically through the eyes of stakeholders has paramount importance to realize a successful integration. Thus, this study aimed to assess the perspectives of the stakeholders of the Eritrean Pharmacovigilance Center (EPC) on the integration of pharmacovigilance activities into the Eritrean healthcare system. Methods An exploratory qualitative assessment of the integration of pharmacovigilance activities into the healthcare system was conducted. Key informant interviews were conducted among the major stakeholders of the EPC via face-to-face and telephone interviews. Data were collected between October 2020 and February 2021, and analyzed through thematic framework analysis. Results A total of 11 interviews were completed. The integration of the EPC in the healthcare system was rated as good and encouraging except in the National Blood Bank, and Health Promotion. The relationship between the EPC and Public health programs was described as mutual with an eminent impact. Several facilitating factors for integration were identified namely: the unique work culture of the EPC; provision of basic and advanced training; motivating and recognizing healthcare professionals in vigilance activities; and the financial and technical support provided to the EPC from national and international stakeholders. On the other hand, the absence of concrete communication systems, inconsistencies in training and communication, the absence of data-sharing mechanisms and policies, and the absence of designated pharmacovigilance focal persons were identified as barriers to successful integration. Conclusion Integration of the EPC in the healthcare system was found to be commendable except in some areas of the healthcare system. Therefore, the EPC should work towards identifying further areas of integration, mitigate the identified limitations and at the same time sustain the integration already initiated.