To reduce NOx emissions from diesel engines, the urea-SCR (selective catalytic reduction) system has been introduced commercially. In urea-SCR, the freezing point of the urea aqueous solution, the deoxidizer, is −11°C, and the handling of the deoxidizer under cold weather conditions is a problem. Further, the ammonia escape from the catalyst and the generation of N2O emissions are also problems. To overcome these disadvantages of the urea-SCR system, the addition of a hydrocarbon deoxidizer has attracted attention. In this paper, a micro-reactor SCR system was developed and attached to the exhaust pipe of a single cylinder diesel engine. With the micro-reactor, the catalyst temperature, quantity of deoxidizer, and the space velocity can be controlled, and it is possible to use it with gas and liquid phase deoxidizers. The catalyst used in the tests reported here is Ag(1wt%)-γAl2O3. First, three gas phase hydrocarbons, LPG, ethylene, DME (Di-methyl ether), were evaluated as deoxidizers. The NOx reduction by DME started around 300 °C catalyst inlet temperature, and 90% of NOx reduction was achieved above 400 °C. The reactivity of ethylene and LPG as the deoxidizer is low, and a higher catalyst inlet temperature, above 450 °C, is required for the SCR to become active. As a liquid deoxidizer, the using of the diesel fuel as a deoxidizer is interesting, but the vaporization of the diesel fuel is a problem for the HC-SCR system. The n-heptane, that has a higher volatility but the same cetane number as diesel fuel, was sometimes used as an alternative of diesel fuel for the combustion research, and applied in this research to investigate the diesel fuel performance as a deoxidizer. The catalyst inlet temperature to achieve 80% of NOx reduction at SV=25000 hr−1 was 400 °C, however, at 350 °C 80% NOx reduction was possible for SV=12500 hr−1. The space velocity of the catalyst is closely related to the NOx reduction performance.