This research article provides a comprehensive scenario analysis of key structural changes in Kazakhstan’s fuel and energy complex subsectors until 2060, focusing on decarbonization efforts. The background places the issue of decarbonization in a broader context, considering the country’s vast size and sparse population. The study’s purpose involves analyzing the development of the climate agenda by comparing two scenarios: a “reference” scenario without decarbonization measures and a carbon neutrality scenario until 2060 (CN2060). A mathematical technical-economic model based on the TIMES paradigm (The Integrated MARKAL-EFOM System) serves as the method to optimize and simulate Kazakhstan’s energy system. The main findings reveal sets of policies, standards, and legislative, economic, and political decisions that are required to achieve CN2060. Additionally, the integration of a low-carbon policy, sectoral and cross-cutting approaches, the impact of the coronavirus crisis, the Russia-Ukraine conflict, and energy security issues receive a discussion. The article concludes with projected shares of generation and investment in renewable energy sources (RES) necessary for attaining CN2060. This work offers novel insights into challenges and opportunities for Kazakhstan’s transition to a low-carbon economy.