The disclosed computer-implemented method for reverse-engineering malware protocols may include (1) decrypting encrypted network traffic generated by a malware program, (2) identifying at least one message type field in the decrypted network traffic, (3) identifying at least one message in the decrypted network traffic with the identified message type, and (4) inferring at least a portion of a protocol used by the malware program by analyzing the identified message to identify a field type for at least one data field of the identified message of the identified message type. Various other methods, systems, and computer-readable media are also disclosed.