A signalling pathway is a cascade of reactions carried out together by a group of molecules in a system to bring out the metabolic functions starting with cell division to cell death. When signalling pathways interact with one another, they form networks, which allow cellular responses to be coordinated, often by combinatorial signalling events. Any abnormal change affecting the activation or deactivation of such signalling events leads to the abnormal physiological cellular functions. The understanding of the molecular mechanism of signalling pathways is beneficial to understand the pathological scenery and treatment. Recent advancements in computational methods have given a new insight to understand the molecular mechanism involved in signalling pathways. The use of systemic and computational tools is crucial in systems biology as the complexity of the biological system is more, a vast amount of data is being generated and the scattered pieces of information has to be integrated into a meaningful order. The present chapter deals with the utilization of systems biology tools, and data mining techniques to understand the molecular mechanism of ‘Wnt signalling pathway; an intercellular pathway which regulates critical aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development’, with the integrated software platforms, which could help to address the future research problems in biology and medicine.