To achieve carbon neutrality by 2050, Malaysian government has identified green hydrogen (H2) as one of the potential energy sources. However, the high production cost of green H2 and technical complications of H2 storage conditions for distribution undermines the strategic framework of the H2 roadmap in Malaysia. The lack of investments in pre-requisite support infrastructure for the H2 production, conversion, and storage technologies impedes the progress of the H2 economy in Malaysia. Recently, ammonia (NH3) has emerged as a promising carbon-free energy carrier due to its increased ease and safety during transportation and storage. There is limited literature regarding the inclusion of an NH3 synthesis and storage loop in green H2 supply chains. This research proposes a systematic approach for the techno-economic evaluation of green H2 supply chains with green NH3 as a clean energy carrier of H2 storage and distribution. A superstructure-based mathematical optimisation model was developed to synthesise the optimum supply chain network configuration for a given optimisation objective. A case study is solved to illustrate the proposed model.