Biomass-based fuels are gaining importance for operating a compression ignition engine as they can curb greenhouse gases and are a key for addressing the energy security. Hydrotreated oil is considered to be a potential drop-in fuel for the compression ignition engine as its cetane number is higher than fossil diesel. In this study, hydrotreated waste cooking oil and its blends (10%, 20%, 30%, 40% and 50% by volume) with diesel were prepared. The ignition probability of the test fuel samples was found using a hot-plate test setup. The neat hydrotreated fuel has higher ignition probability at a particular temperature than the other test fuels. The Sauter mean diameter of the test fuels was also observed using a Malvern Spraytec test setup. The results reveal that the neat hydrotreated fuel has higher Sauter mean diameter due to its high viscosity. As the percentage of the hydrotreated fuel in the blend decreases, the Sauter mean diameter decreases and diesel has the lowest Sauter mean diameter. The test fuels were also used to run a compression ignition engine. The results reveal a decrease in brake thermal efficiency with the increase in the hydrotreated fuel share in the blend. The heat release for the blends starts earlier than diesel and the peak heat release is also lower than diesel. The HC, CO and smoke emissions for the test blends decreases up to 30% blend. When the percentage of the hydrotreated oil is further increased, the emissions starts increasing. The NO emissions were lower than diesel for all the test samples. As compared to diesel, the maximum reduction in NO (neat), HC (30% blend), CO (30% blend) and smoke emissions (30% blend) is 23.2%, 14.4%, 13.83% and 13.3%, respectively.