In the last decade, numerous technologies have been developed to convert biomass into value-added products (bioenergy, biomaterial and biochemical). However, not much research has been done in the identification of possible pathways to convert biomass into pharmaceutical products. This research focuses on exploiting the potential pharmaceutical products that can be derived from palm-based biomass. However, due to the large number of potential products, multiple reaction pathways and processing technologies involved. Thus, there is a need for a systematic methodology which is capable to identify the optimal production routes in the integrated biorefinery based on different optimisation objectives. In this work, a mathematical optimisation-based approach is developed to determine the optimum conversion pathway that converts palm-based biomass into pharmaceutical products with maximum economic performance. Besides, a novel approach which can estimate the operating cost of pharmaceutical products is also introduced in this work. In addition, sensitivity analysis is carried out to investigate the impact of changes in conversion of reaction, market price and operating cost to the economic performance of the synthesised integrated biorefinery.