Disclaimer: I work for Redgate Software as a Technical Lead for database comparison technologies in Flyway.

Support for Table Partitioning in PostgreSQL for Flyway was added on 14th May 2025 (see Flyway Desktop release notes).

Please update to the latest version of Flyway and Flyway Desktop and you will be able to source control, manage and deploy your table partitions changes using Flyway. If you have any issues, don't hesitate to contact our support team.