The purpose of this study is to determine the socio-economic and demographic factors of intra-regional inequality in Kazakhstan and their implications for cluster-based innovation in healthcare. A hybrid approach has been used, consisting of a systematic review of 181 publications using the PRISMA 2020 protocol and econometric analysis of the 2001–2024 panel data for the districts of Kazakhstan, consisting of 3,842 observations. Fixed-effects, cluster-robust, and hierarchical mixed-effects models were employed using standardized variables of population size, fertility, mortality, migration, criminality, and investments. The results reveal that the strongest and most robust predictor of intra-regional inequality in Kazakhstan is investment in fixed capital (β = 0.466, p < 0.01; β = 0.399, p < 0.01). Population size has consistently negative effects on intra-regional inequality in Kazakhstan (β = –0.240 to –0.256, p < 0.05 and p < 0.01). In the multilevel model, fertility increases intra-regional inequality in Kazakhstan (β = 0.114, p < 0.01), whereas mortality and net migration decrease it (β = –0.150 and β = –0.037, p < 0.01). The model explained 37.1% of the variance in intra-regional inequality in Kazakhstan (R² = 0.371). The results suggest that without balanced investment and territorially differentiated policies, cluster-based innovation in healthcare can even reinforce rather than alleviate regional disparities.