ABSTRACT The purpose of the article is to substantiate the theoretical, methodological, and conceptual foundations for managing innovative activities in the healthcare system of the Republic of Kazakhstan and develop recommendations aimed at improving its effectiveness in modern conditions. This study employs a mixed-method approach, integrating retrospective analysis, statistical evaluation, and economic analysis to examine trends and performance in healthcare innovation within Kazakhstan. It utilizes dynamic and structural analysis to assess innovation effectiveness and identifies key factors influencing innovative activity through equity participation and ranking methods, underpinning recommendations for improved management practices. This article critically concludes that healthcare innovation in Kazakhstan must address the low effectiveness of current innovative activities, hindered primarily by insufficient demand and funding constraints. The study underscores the essential role of a robust management mechanism focused on resource allocation, service delivery efficiency, and digital technology integration. It highlights the necessity for strategic funding distribution, enhanced international cooperation, and leveraging higher education institutions for innovation drive. The findings advocate for comprehensive strategies to boost innovation’s commercial efficiency and suggest further research on implementing these strategies in the context of Kazakhstan’s unique socioeconomic landscape and healthcare needs. Priority recommendations aimed at improving the efficiency of managing the country’s healthcare innovation activities have been formed. The results obtained in the study can be useful both to the scientific community and to managers at various levels in the healthcare sector.