This work involves a with comparative study of smoke emission reduction methods of a compression ignition engine fueled with neat Waste Cooking Oil (WCO). The test engine chosen for this study is an agricultural based single cylinder, with a variable compression ratio, which is water cooled and is of the direct injection compression ignition engine type. Initially the test engine was tested using with neat diesel and WCO using various load conditions with three different compression ratios, i.e., 16.5, 17.5 and 18 for its performance, emission and combustion behaviours respectively. Results revealed that, both diesel and neat WCO experienced higher Brake Thermal Efficiency (BTE) with increased compression ratio. Except for smoke emission, all other carbon based emissions of neat WCO was found to reduce with increased compression ratio. In view of the above identified problems, a fuel and engine level modification was carried out introduce to the best practice of operating the engine with least smoke emission. Emulsion and injection timings were chosen as two parameters, and their influence on the smoke emission of the engine operated with neat WCO was studied. Standard injection timing (i.e. 23oBTDC) of the engine was increased by a maximum of four degrees at an interval of 2o crank angle. Subsequently, an emulsion was made with neat WCO and tested in the engine for smoke emission. Comparison of the results of smoke emission obtained after implementing the two different control methodologies, showed a higher percentage of smoke emission reduction (i.e. 25%) with respect to emulsified WCO when compared to the advancement of injection timing. Emulsification method also obtained the benefits of reduced oxides of nitrogen emission of neat WCO. However, the BTE was reduced marginally (i.e. 8%) when emulsified fuels were used which improved with advancement of injection timing. Hence, this work suggests that emulsification techniques will be a better choice for operating the engine when the reduction of smoke emission is considered as the prime objective whereas for the optimized operation, it is suggested that advancement of injection timing be used as a correct choice for operating the engine with neat WCO.