A computer-implemented method for maintaining encrypted search indexes on third-party storage systems may include (1) identifying a plurality of encrypted files, (2) identifying a plurality of keywords contained in the plurality of encrypted files, and (3) generating an encrypted search index for searching the plurality of encrypted files by (i) identifying, for each keyword in the plurality of keywords, a list of encrypted files in the plurality of encrypted files that contain the keyword, (ii) encrypting the list of encrypted files, and (iii) storing the encrypted list of encrypted files such that the encrypted list of encrypted files can be identified using a lookup key generated by applying a pseudo-random function to the keyword. Various other methods, systems, and computer-readable media are also disclosed.