To combat global warming, many industrialized countries have announced plans to ban vehicles powered by fossil fuel in the near future. In alignment with this global initiative, many countries across the globe are committed to decarbonizing their public transportation sector, which significantly contributes to increased greenhouse gas emissions. A promising strategy to achieve this goal is the adoption of electric buses, specifically battery electric buses and fuel cell electric buses. Each technology offers distinct advantages and drawbacks, making the decision-making process complex. This research aims to answer two critical questions: What is the optimal choice for decarbonizing the bus transportation sector—electric battery buses or fuel cell electric buses? And what are the best energy carrier pathways for charging or refueling these buses? We propose a methodological framework based on multi-criteria decision-making to address these questions comprehensively. This framework utilizes the entropy weighting and the Technique for Order Preference by Similarity to the Ideal Solution (TOPSIS) methodologies to rank alternative bus technologies along with energy carrier pathways. The framework evaluates a range of criteria, including economic viability, energy demand, and environmental aspects. To illustrate the framework, we considered Qatar as a case study. Our results indicate that, with respect to economic viability and energy consumption, the operation of battery electric buses is favored over fuel cell electric buses, regardless of the energy pathway utilized during both the energy production and bus operation phases. However, from an environmental perspective, operating both bus alternatives using energy from green sources provides superior performance compared to when these buses are powered by natural gas sources.