The present research is a comprehensive study of nuclear fuel cycle scenarios for the India-Japan Civil Nuclear Cooperation. Authors explained the nuclear fuel cycle strategies. This paper extensively covers the role and importance of the Thorium fuel cycle to be explored as a part of future nuclear fuel cycle in the implementation phase under the India-Japan Civil Nuclear Cooperation. In this research, authors are emphasizing on the common factors to be evaluated in the nuclear fuel cycle for the Indian and Japanese nuclear power programmes. This paper examines the Indian and Japanese nuclear fuel cycle scenarios. The authors have discussed the mutual offerings between India and Japan in detailed manner to develop the civilian nuclear fuel cycle jointly.