A method of manufacturing a fatty acid alkyl ester by reacting a fatty acid and/or a triglyceride and an alcohol in the presence of a solid acid catalyst, the method of manufacturing a fatty acid alkyl ester being characterized by including: a first reaction step of producing a fatty acid alkyl ester reaction solution A by contacting the fatty acid and/or the triglyceride and the alcohol with the solid acid catalyst at a temperature of 100 to 250°C and a pressure of 0.1 to 6.0 MPa; a first separation step, following on said first reaction step, of removing said alcohol, water and glycerol from said fatty acid alkyl ester reaction solution A, to produce a crude fatty acid alkyl ester A having a water concentration of no greater than 0.1 mass%; a second reaction step of contacting said crude fatty acid alkyl ester A and said alcohol with the solid acid catalyst at a temperature of 60 to 210°C at a pressure of 0.1 to 6.0 MPa; and a second separation step of further removing said alcohol, water and glycerol from a fatty acid alkyl ester B produced in the second reaction step, to produce a fatty acid alkyl ester B having a free glycerol concentration of no greater than 0.02 mass%; wherein the solid acid catalyst is produced by impregnating, on at least one inorganic porous carrier selected from the group consisting of silica, alumina, or a combination thereof; an oxide of at least one metallic element selected from the VIb group of the periodic table; an oxide or sulfate of at least one metallic element selected from the group consisting of manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), gallium (Ga) and tin (Sn); and an oxide of at least one nonmetallic element selected from boron and silicon, characterized in that said oxide, oxide or sulfate and oxide are simultaneously impregnated to said inorganic porous carrier, wherein, with respect to the inorganic porous carrier, the amounts of the metal oxide, the metal oxide or sulfate and the nonmetal oxide impregnated, as calculated for the highest metal oxide, are 2.5 to 25 mass%, 1 to 10 mass%, and 0.5 to 5 mass%, respectively, and the total of, and is no greater than 30 mass%. a first reaction step of producing a fatty acid alkyl ester reaction solution A by contacting the fatty acid and/or the triglyceride and the alcohol with the solid acid catalyst at a temperature of 100 to 250°C and a pressure of 0.1 to 6.0 MPa; a first separation step, following on said first reaction step, of removing said alcohol, water and glycerol from said fatty acid alkyl ester reaction solution A, to produce a crude fatty acid alkyl ester A having a water concentration of no greater than 0.1 mass%; a second reaction step of contacting said crude fatty acid alkyl ester A and said alcohol with the solid acid catalyst at a temperature of 60 to 210°C at a pressure of 0.1 to 6.0 MPa; and a second separation step of further removing said alcohol, water and glycerol from a fatty acid alkyl ester B produced in the second reaction step, to produce a fatty acid alkyl ester B having a free glycerol concentration of no greater than 0.02 mass%; wherein the solid acid catalyst is produced by impregnating, on at least one inorganic porous carrier selected from the group consisting of silica, alumina, or a combination thereof; an oxide of at least one metallic element selected from the VIb group of the periodic table; an oxide or sulfate of at least one metallic element selected from the group consisting of manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), gallium (Ga) and tin (Sn); and an oxide of at least one nonmetallic element selected from boron and silicon, characterized in that said oxide, oxide or sulfate and oxide are simultaneously impregnated to said inorganic porous carrier, wherein, with respect to the inorganic porous carrier, the amounts of the metal oxide, the metal oxide or sulfate and the nonmetal oxide impregnated, as calculated for the highest metal oxide, are 2.5 to 25 mass%, 1 to 10 mass%, and 0.5 to 5 mass%, respectively, and the total of, and is no greater than 30 mass%.