To provide an effective energy transition, hydrogen is required to decarbonize the hard-to-abate industries. As a case study, this paper provides a holistic view of the hydrogen energy transition in the United Arab Emirates (UAE). By utilizing the directional distance function undesirable data envelopment analysis model, the energy, economic, and environmental efficiency of UAE sectors are estimated from 2001 to 2020 to prioritize hydrogen sector coupling. Green hydrogen production efficiency is analyzed from 2020 to 2050. The UAE should prioritize the industry and transportation sectors, with average efficiency scores of 0.7 and 0.74. The decomposition of efficiency into pure technical efficiency and scale efficiency suggests policies and strategies should target upscaling the UAE’s low-carbon hydrogen production capacity to expedite short-term and overall production efficiency. The findings of this study can guide strategies and policies for the UAE’s low-carbon hydrogen transition. A framework is developed based on the findings of the study.