Background: Non-communicable diseases (NCDs) are significant causes of morbidity and mortality in Malawi and are the second leading cause of deaths in adults after HIV and AIDS. The purpose of this assessment was to identify human, infrastructural and systems requirements in implementation research to support the response to the NCD epidemic in the Malawian health sector.Methods: This national needs assessment was conducted using a concurrent triangulation mixed methods approach. Twenty-two health facilities providing tertiary (n =4), secondary (n =2) and primary (n = 16) care level were included in the assessment. Qualitative interviews with 72 participants from the health facilities, academic institutions, development partner organizations, Ministry of Health and the Central Medical Stores Trust from across the country were also conducted. Descriptive statistics were used to analyze the quantitative data from the facility assessment and thematic content analysis was done to identify themes from the qualitative data. Results: The qualitative and quantitative findings were merged and categorized into five thematic areas. Theme 1: Record keeping and surveillance for NCDs – which showed a high incidence of hypertension and diabetes at the facilities. Theme 2: Availability of NCD services- 15 (68%) facilities had an NCD clinic available. NCD clinics were reported available at 75% of the tertiary facilities, 100% of secondary facilities and 63% of the primary facilities. Theme 3: Perceived needs for improving NCD care – where key informants highlighted the need for more human resources, drugs, guidelines and diagnostic technologies. Theme 4: Limited NCD focused implementation research engagement. This was due to lack of funding and limited number of researchers conducting NCD focused research. Theme 5: Opportunities for improving NCD focused implementation research. Opportunities were available through the growing interest and focus on NCDs by the government and development partners.Conclusion: NCDs are a significant health burden in the Malawian healthcare services. A general lack of human, systems and material resources in the healthcare system negatively affects extent of coverage of NCD services and implementation research activities necessary for improving care.