Malaysia has committed to achieving net-zero emission by 2050, as outlined in the National Energy Transition Roadmap (NETR). While nuclear energy is not currently part of the energy mix under the National Energy Policy 2022–2040, its inclusion could significantly contribute to decarbonization. This study evaluated nuclear power’s potential role in Malaysia’s energy transition using the reference approach to estimate carbon emission in 2050 and compared these results with NETR projections. CO₂ emission from fossil fuels was calculated to determine the residual CO₂ emission. The number of nuclear power plants needed to offset the residual CO₂ emission was then calculated for analysis. The levelized cost of electricity (LCOE) was assessed using the IAEA simple INPRO Nuclear Energy System (NES) simulator for different discount rates and deployment scenarios. Results indicated that under the reference approach, 34 reactors would be required to offset residual emission after accounting for land use, land-use change, and forestry (LULUCF) sinks, whereas using NETR projections would require 18 reactors. However, construction timelines and licensing constraints pose significant challenges in deploying this huge number of nuclear reactors. A more realistic build rate of one reactor every three years from 2035 would result in six reactors by 2050, avoiding 10.45 Mt CO₂ annually. LCOE values range from $0.04/kWh to $0.10/kWh, depending on discount rate and deployment scale, demonstrating economic competitiveness of nuclear energy. Unfortunately, six nuclear power plants by 2050 are still not enough to achieve net-zero emission even with carbon capture and storage (CCS) projections from NETR being considered.