This study investigated the effect of external carbon source and bed turnover rate on biological denitrification in the pilot-scale IPNR (Ilshin Phosphorus and Nitrate Removal) process. IPNR process is an up-flow reactor filled with Si-media which removes phosphorus physically and nitrate nitrogen biologically using secondary effluent from sewage treatment plant. Phosphorus (PO4-P) was removed using HFO (Hydrous ferric oxide) by adsorption as well as nitrate nitrogen (NO3-N) was transformed to nitrogen gas (N2) by denitrifying bacteria using external carbon source in the same reactor. Methanol was used as an external carbon source for denitrification with various dosing concentration and Si-media bed turnover rate was varied from 6.4 ~ 7.75 day-1. The concentrations of PO4-P and NO3-N in the secondary effluent were from 0.1 to 1.75 mg/L and from 1.1 to 31.9 mg/L, respectively. The results demonstrated that high amount of NO3-N removed from 31.9 to 1.2 mg/L, at the same time PO4-P removed from 1.75 to 0.41mg/L using secondary effluent. Denitrification was found more stable with 6.4 bed turnover/day and 130% over dosing of theoretical methanol dose for denitrification.