This research encompasses a comprehensive study on the application of 1D photonic crystal-based detection in the context of infectious diseases, specifically targeting malaria stages, chikungunya, and dengue. It explores the interactions between the photonic crystal and various biomolecules associated with these diseases, with a focus on platelets, plasma, and uric acid. The transmission spectrum graphs obtained from these interactions provide crucial insights into the detection and quantification of the diseases, offering real-time and label-free monitoring capabilities. Maximum sensitivity of 550 nm RIU−1 and Q factor of 29,260 obtained. Additionally, the study incorporates the design and analysis of a microfluidic channel optimized for the proposed sensor, ensuring accurate temperature and pressure distributions. The results demonstrate the feasibility of the microfluidic platform for enhancing sensor performance and fluid handling. This integrated approach shows promising potential for early disease diagnosis and monitoring, paving the way for practical implementation and further advancements in the field of sensing and diagnostics