Background; Despite the adoption of Elimination of mother to child transmission (EMTCT) strategy in 2012, mother to child transmission of HIV remains one of the significant forms of new HIV infections among children in Uganda, accounting for 20% of new infections. However, the implementation of the EMTCT strategy in Uganda remains unclear and an under researched field. This study aimed at assessing the extent of implementation of EMTCT strategy, barriers and constraints in Lira district using the adapted Policy Implementation Barometer (PIB) approach. Methods; This was a cross sectional study that employed both quantitative and qualitative data collection methods. A Policy Implementation Barometer tool developed by a project called Supporting Policy Engagement for Evidence-based Decisions (SPEED) for Universal Health Coverage in Uganda was adopted to assess the extent of implementation of EMTCT strategy. A total of 32 interviews with health facility managers were purposively conducted from a random sample of 20 health facilities offering Antenatal clinic (ANC) services in Lira district. Quantitative data was analyzed using STATA 14. Qualitative data was analyzed using thematic content analysis approach. Results; Majority 17/32 (53.1%) of the respondents were health facility in charges, 14/32 (43.8%) were midwives and half 16/32 (50.0%) had been in service for more than five years. Half of the respondents perceived their facilities to have fully established programs for implementing EMTCT and only 2/32 (6.2%) perceived the EMTCT programs to be functioning optimally. The perceived level of EMTCT implementation was 80%. Almost all the respondents perceived the funding for EMTCT activities to be inadequate, untimely, and not sustainable. Only 4/32 (12.5%) of the respondents believed that the health workforce size was adequate to support EMTCT activities, 13/32 (40.6%) believed that health workers lacked the skills to provide EMTCT services.Conclusion/Recommendation; Overall, the perceived extent of EMTCT policy implementation was high, however slow progress was reported in some of the key policy objectives due to a number of hindrances including inadequate staff and funding. Therefore, there is a need for strategies to increase the number of health workers for EMTCT and solicit for more funding for the implementation of EMTCT strategy.