The aim of the present study is to analyze the performance, emission and combustion characteristics of a variable compression ratio (VCR), compression ignition (CI) engine using a suitable biodiesel as fuel. The biodiesel selected to conduct this experimental investigation is Karanja biodiesel. The selection of Karanja biodiesel is based on an extensive review of literature which indicated that this is relatively unexplored as fuel on a VCR diesel engine. The experimental analysis is followed by a computational study consisting of optimization and modeling for predicting the optimum performance parameters and emission constituents of the engine. The experimental study is conducted on a four stroke, VCR diesel engine using Karanja biodiesel and its blends with diesel. The thermal performance and emissions characteristics are evaluated by operating the engine at different preset compression ratios(CRs) of 14, 15, 16, 17, 17.5 and 18, different injection pressures (IPs) of 150 bar, 200 bar and 250 bar and varying loads from 0kg to 12 kg in steps of 3kg.The thermal performance parameters evaluated are brake thermal efficiency(BTHE), brake specific fuel consumption(BSFC), BMEP, HBP etc.