The energy planning process essentially requires addressing diverse planning objectives, including prioritizing resources, and the estimation of environmental emissions and associated health risks. This study investigates the impacts of atmospheric pollution for Pakistan from the energy production processes under various modalities. A national-scale bottom-up energy optimization model (Pak-TIMES) with the ANSWER-TIMES framework is developed to assess the electricity generation pathways (2015–2035) and estimate GHG emissions and major air pollutants, i.e., CH4, CO, CO2, N2O, NOX, PM1, PM10, PM2.5, PMBC, PMOC, PMTSP, SO2, and VOC under five scenarios. These scenarios are: BAU (business-as-usual), RE-30 (30% renewables), RE-40 (40% renewables), Coal-30 (30% coal), and Coal-40 (40% coal). It is revealed that to reach the electricity demand of 3091 PJ in 2035, both the Coal-30 and Coal-40 scenarios shall cause maximum emissions of GHGs, i.e., 260.13 and 338.92 Mt (million tons) alongside 40.52 and 54.03 Mt emissions of PMTSP in both of the scenarios, respectively. BAU scenario emissions are estimated to be 181.5 Mt (GHGs) and 24.30 Mt (PMTSP). Minimum emissions are estimated in the RE-40 scenario with 96.01 Mt of GHGs and 11.80 Mt of PMTSP, followed by the RE-30 scenario (143.20 GHGs and 17.73 Mt PMTSP). It is, therefore, concluded that coal-based electricity generation technologies would be a major source of emission and would contribute the highest amount of air pollution. This situation necessitates harnessing renewables in the future, which will significantly mitigate public health risks from atmospheric pollution.