Even though intellectual capital (IC) represents the crucial element of enterprises' high-above performance and sustainable competitive advantage, there is a lack of systematic approach to understanding whether there are significant differences in the IC of manufacturing and services enterprises. The research analysis is performed using data collected from 224 respondents representing managers in enterprises of the Republic of Srpska, Bosnia and Herzegovina. Exploratory factor analysis (EFA), as an applied statistical technique, identifies the IC components. To address the research question, the statistical difference in means was tested for each IC component in manufacturing and service enterprises using appropriate parametric t-test and non-parametric Mann-Whitney U test for two independent samples. The research results reveal that service enterprises have higher human, relational and renewal capital than manufacturing enterprises. Structural capital has a more pronounced role in manufacturing enterprises. As enterprises move towards service orientation, they need to rearrange their approach to IC stocks and management, and acknowledging that differences between manufacturing and service enterprises are present represents the first step. Research findings shed new light on the differences between these enterprises in IC possession and management.