The present invention relates to an apparatus for processing silica-containing wastewater with increased processing efficiency, which comprises: a first gravitational precipitation tank (10) receiving the silica-containing wastewater to firstly precipitate and remove silica; a second gravitational precipitation tank (20) installed at the rear end of the first gravitational precipitation tank and precipitating and removing the remaining silica included in the processed water; an aerobic membrane separation tank (30) installed at the rear end of the second gravitational precipitation tank and aerating the inflow processed water to perform solid-liquid separation and nitrification of the processed water; a deaeration tank (40) installed at the rear end of the aerobic tank to reduce dissolved oxygen included in the inflow processed water; and a reaction tank (50) receiving the processed water transferred from the deaeration tank to denitrify nitride and nitrogen included in the processed water. According to the present invention, the apparatus can effectively process silica generated from a semiconductor, particularly a wafer process, and can simultaneously process nitrogen and phosphorous, which are nutrient salts, and organic materials included in the wastewater.