Background The objectives of the study reported in this paper were: (a) to score the coverage of core NCD population-based interventions and individual services in Mauritius; (b) to analyse and score the presence of 15 common health system challenges that impede delivery of core NCD interventions and services in Mauritius; and (c) to provide policy recommendations for Mauritius to address health system barriers to delivery of NCD interventions and services. Methods The Mauritius country assessment applied the guidelines developed by the World Health Organization Regional Office for Europe for systematically scoring coverage of NCD interventions and assessing health system challenges for improving NCD outcomes. The assessment used qualitative research design approach. Results Of the 24 core population-based interventions for addressing key NCD risk factors, 16.7% were rated extensive, 37.5% moderate and 45.8% limited. Three (20%), 8 (53%) and 4 (27%) of the 15 individual/personal CVD, diabetes and cancer services were rated extensive, moderate and limited respectively. The top five health system challenges hampering scale-up of coverage of population-based NCD interventions in Mauritius were inadequate interagency cooperation; limited application of explicit priority setting approaches; inadequate change management; sub-optimal distribution and mix human resources; insufficient population empowerment; and insufficient political commitment. The top five challenges had average scores of between 3.1 (interagency cooperation) and 2.4 (distribution and mix of human resources). The top five health system challenges constraining expansion in coverage of individual NCD services were limited integration of evidence into practice; limited use of explicit priority-setting approaches; inadequate application of information and technology solutions; insufficient population empowerment; and sub-optimal distribution and mix of human resources. The top five challenges for individual interventions had mean scores varying between 2.6 (integration of evidence into practice) and 1.7 (distribution and mix of human resources). Conclusions Mauritius needs to increase its domestic general government investments into the national health system and requisite multi-sectoral action to address the priority health system challenges with a view of bridging the existing gaps in coverage of NCD population-based interventions and individual services.