The present consumption rates and heavy dependence on fossil fuels pose a humongous threat to the environment. The increased pollution in urban areas is already causing serious sociological, ecological and economic implications. The issue of energy security led governments and researchers to look for alternate means of renewable and environment friendly fuels. Biodiesel has been one of the promising, and economically viable alternatives. The biodiesels are reported to cause reduction in CO, HC and PM emissions. However, NOx emissions are increased in case of biodiesel in CI engine. Therefore, a Urea-SCR over Fe-ZSM5 honeycomb substrate (400cpsi) zeolite catalyst after treatment system is an effective technology to reduce emissions for biodiesel applications. Exhaust gases pass through the catalyst and reactions take place along its surface, consequently converting NOx into nitrogen and H2O. This conversion compliments the functioning of fish oil biodiesel in reducing the overall emissions. Taking a lead from this, the present study focuses on evaluation of performance and emission characteristics of a medium capacity diesel engine on blends of fish oil biodiesel and diesel employing Urea-SCR. The relationship of urea injection distance from the SCR catalyst in the exhaust pipe is also studied. Fish oil was trans-esterified with methyl alcohol to produce methyl ester. B20 blend of biodiesel was used since it balances the property differences with conventional diesel e.g. performance, emission benefits and cost. Further, B20 blend can be used in automotive engines with no major modification. To produce Urea injection in the exhaust pipe, a solution of urea (32.5%w/w) with water was sprayed using electronic injectors. Fe-ZSM5, honeycomb structure substrate (400cpsi) was used as the SCR catalyst. Fe-ZSM5 was used due to its high activity in the working temperature regime of the current paper. The fuel, F20 and diesel, were tested in CI engine, one at a time, with and, without Urea-SCR. The distance of Urea injection in the exhaust pipe was also varied and related performance and emissions were studied in each case. The results showed that the use of F20 with SCR reduces NOx as compared to the absence of SCR, without compromising on the thermal efficiency and other emissions. Also the greater distance of injection from the SCR unit has been found to be beneficial for NOx reduction.