The present invention provides a method for producing a fatty acid ester inexpensively and efficiently by reacting a lipase or an intact mircroorganism containing a lipase, an oil and fat, and a linear lower alcohol in a system containing little or no solvent in the presence of water. The intact microorganism has not been treated with a solvent or the like, and is used as such, so that a fatty acid ester can be prepared in a simple manner. An oil and fat, a natural oil and fat such as a vegetable oil and fat, an animal oil and fat, as well as a waste oil thereof can be used. According to the method of the present invention, a reaction proceeds even in the presence of water, so that waste oils containing a large amount of water can be used as a raw material. Therefore, the waste oil to be dumped into the environment can be recycled, and a biodiesel fuel, which hardly pollutes the environment, can be provided at the same time.