A system and method for transferring data between different types of systems, and in particular uses log-based replication to transfer data between different types of systems. In accordance with an embodiment, the system can be used to perform a one-time or initial copy of the MySQL data from a source database system to a target database system, and/or to replicate the on-going transactions captured from a MySQL database's binary log into one or additional non-MySQL database(s) on a continuous basis, such that the two systems are synchronized for transactions of interest. In accordance with an embodiment, full or partial data changes can be extracted from the MySQL binary log, optionally transformed, skipped or augmented, output or written to a file, and then applied at any of one or more target systems (e.g. another MySQL database, or a non-MySQL database), thereby synchronizing the source and target systems.