Energy is typically generated from fossil fuels, leading to significant greenhouse gas (GHG) emissions. Therefore, cleaner energy needs to be used to reduce GHG emissions in the energy sector. Hydrogen (H2) is identified as a potential resource suitable for replacing fossil fuels as H2 burns with oxygen to produce water (H2O) and generates no emissions as a result of this. However, H2 is normally produced through steam reforming of natural gas, which is a fossil fuel. Clean H2 can be produced if its derived from renewable pathways, such as solar powered water electrolysis, gasification of biomass, etc. However, determining a feasible renewable pathway is challenging. In addition, storage of H2 is another challenge as the energy density of H2 is considerably low. To increase the energy density, H2 must stored at high pressure and low temperature. This causes high storing costs for H2 before being transported to the end-users and high energy consumption requirements. H2 production from renewable sources is also lower in efficiency when compared with conventional production technology. Thus, it is critical to develop a systematic optimisation tool to analyse and optimise the production of clean H2 to overcome the abovementioned challenges. This work presents an optimisation model to optimise the production of clean H2 based on total annualised cost, yield, efficiency, storage and energy consumption of each technology. To illustate the proposed model, a case study with several scenarios, such as an economically feasible and clean H2 process and optimal H2 production and storage technologies in terms of energy consumption, is solved.