A method for preparing permanently hydrophobic aerogel and permanently hydrophobic aerogel prepared by the method. The method comprises adding sodium silicate to HCl at 30 to 90° C. until an acidity reaches pH 3-5, to form silica hydrogel under acidic conditions of pH 3-5, washing the silica hydrogel with distilled water using a mixer, followed by filtering, adding the silica hydrogel to a silylating solution of silylating agent in n-butanol at pH 1-5 using an acid selected from hydrochloric acid, sulfuric acid, phosphoric acid and nitric acid, to simultaneously conduct silylation and solvent replacement, and drying the silica hydrogel; The method has the following advantages; i) silylation and solvent replacement can be simultaneously conducted, ii) n-butanol is used as a reaction solvent instead of methanol upon silylation, thus obtaining a thermal conductivity comparable to conventional aerogel powders, iii) silylation is conducted under improved conditions, i.e., strong acidic conditions of pH 1-5, and as a result, all of the aerogel powders can be reacted with a silylating agent, thereby obtaining permanently hydrophobic aerogel, iv) the washing with a mixer makes the amount of removed sodium ions uniform, thus it is suitable for mass-production, and v) the method provides a relatively simplified procedure and the use of the silylating agent in a small amount enables low costs and mass-production.