Transit agencies are always seeking opportunities to conserve fuel (which typically provides simultaneous emissions reductions). According to the 2010 national bus transportation statistics for the United States, deadhead trips cover 13.3% of a total of 2.4 billion transit bus miles. Therefore, reducing deadheading tends to be a promising alternative to achieve reduction of fuel consumption and emissions. In order to minimize fuel consumption and emissions related to deadheading, this study proposes three strategies including optimal assignment of buses to existing bus yards, relocating a bus yard to a better location, and constructing a new bus yard. The Metropolitan Atlanta Rapid Transit Authority (MARTA) is taken as an example for analysis these three scenarios and the effectiveness of each strategy is evaluated in terms of fuel saving, emissions reduction, and cost impacts. Bus assignment and yard selection are conducted through GIS-based network analysis. Potential improvements on fuels and emissions are quantified through MOVES-Matrix, a high-performance emission simulation platform built based on MOVES model, with real-world operations data applied. Cost impacts relate to transit facility and operating costs. The results show that relocating the current yard is the “winning” strategy in perspective of emissions in the long run; however, re-assigning buses achieves 6% reduction in fuel consumption and does not require additional expenditures. The paper showcases the strategies for reducing deadheading in the planning process for transit agencies, and the analysis herein, conducted for the Atlanta region, can be easily applied to other agencies across the nation.