Abstract Background The National Plan for Malaria Elimination (NPME) in Myanmar (2016–2030) aims to eliminate indigenous Plasmodium falciparum malaria in six states/regions of low endemicity by 2020 and countrywide by 2030. To achieve this goal, in 2016 the National Malaria Control Program (NMCP) implemented the “1-3-7” surveillance and response strategy. This study aims to identify the barriers to successful implementation of the NPME which emerged during the early phase of the “1-3-7” approach deployment. Methods A mixed-methods study was conducted with basic health staff (BHS) and Vector Born Disease Control Program (VBDC) staff between 2017 and 2018 in six townships of six states/regions targeted for sub-national elimination by 2020. A self-administered questionnaire, designed to assess the knowledge required to implement the “1-3-7” approach, was completed by 544 respondents. Bivariate analysis was performed for quantitative findings and thematic analysis was conducted for qualitative findings using Atals.ti software. Results Although 83% of participants reported performing the key activities in the “1-3-7” surveillance and response approach, less than half could report performing those activities within 3 days and 7 days (40 and 43%, respectively). Low proportion of BHS correctly identified six categories of malaria cases and three types of foci (22 and 26%, respectively). In contrast, nearly 80% of respondents correctly named three types of case detection methods. Most cited challenges included ‘low community knowledge on health’ (43%), ‘inadequate supplies’ (22%), and ‘transportation difficulty’ (21%). Qualitative data identified poor knowledge of key surveillance activities, delays in reporting, and differences in reporting systems as the primary challenges. The dominant perceived barrier to success was inability to control the influx of migrant workers into target jurisdictions especially in hard-to-reach areas. Interviews with township medical officers and the NMCP team leaders further highlighted the necessity of refresher training for every step in the “1-3-7” surveillance and response approach. Conclusions The performance of the “1-3-7” surveillance and response approach in Myanmar delivers promising results. However, numerous challenges are likely to slow down malaria elimination progress in accordance with the NPME. Multi-stakeholder engagement and health system readiness is critical for malaria elimination at the sub-national level.