BackgroundClinical Pharmacy Services (CPS) are a reality in many health systems around the world. However, there are few studies that discuss the facilitators and the strategies to implement CPS in healthcare systems. In this way, the objective of this study was to identify the facilitators and strategies involved in the CPS implementation process in some public health units in a metropolis in the Northeast Brazil.MethodsA qualitative study was carried out with health-system pharmacists and managers who experienced the implementation of CPS. Therefore, focus groups were conducted with pharmacists, and the interviews with the managers. The discussions were carried out through semi-structured scripts and were recorded in audio and videos, after the signature of the consent form. The recordings were transcribed and analyzed independently through content analysis, followed by consensus meetings between researchers.ResultsTwo focus groups were conducted, with an average of seven pharmacists per group, and five interviews with local health managers. Participants reported 39 facilitators who were related to the categories: local healthcare network, healthcare team, pharmacists and implementation process of the CPS. And 21 strategies attributed to the following categories: local healthcare network, pharmacists and implementation process of the CPS.ConclusionsThis study identified facilitators and strategies of the implementation of CPS. Most of the positive experiences were related to the clinical skills and proactive attitudes of pharmacists. These findings may support pharmacists and health managers to implement CPS in health systems.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3403-4) contains supplementary material, which is available to authorized users.