For long, this station was considered to have two major limitations:

1. The island platforms, at 675-feet-long, could accommodate trains of no more than ten carriage length.
2. The location of the site was thought to be too distant from the top end of Rochester High Street, where the main tourist attractions of the castle and cathedral are situated.

The advent of selective door opening on main line stock addressed point 1, potentially allowing formations which were longer than ten vehicles to stop at the station. However, this practice resulted in the points giving access to adjacent platforms being fouled by overhanging carriages. Any attempt to lengthen the platforms would be coupled with substantial engineering works given the station's location upon a viaduct, which made it difficult to extend "up" and "down" loops.

A solution to the aforementioned drawbacks of the station were published in January 2010 in a Network Rail Route Utilisation Strategy. This outlined building a replacement station 500 yards to the north of the existing platforms, partially on a site which was at that time used as a council car park. This was advantageous, for the works could be made to coincide with the East Kent Resignalling Scheme, allowing track layout changes and infrastructure renewal to be addressed in one go.

A formal planning application made by Network Rail for a new station was approved by Medway Council in September 2013. In November of that year, the first signs of work emerged at the site, starting with vegetation clearance along the embankment. More information on the new site can be found in the Rochester (New) section, but in brief, by the end of 2014, a new underpass had been installed through the embankment and an island platform was taking shape.

The old station was scheduled to close in the early hours of 13th December 2015. However, the final train in fact departed at 00:56 the previous day; weekend engineering works saw a rail replacement bus service in place for Saturday and most of Sunday. The new station formally opened at 17:00 on Sunday 13th December, the first departure being the 17:21 to London Victoria (ex-Dover Priory and Herne Bay).

The ultimate plan is to demolish the old station's platforms (can a new home be found for the surviving SE&CR canopy and railings on the "up" side?), but retain the main building of 1892 origin. As a result of delays completing the resignalling project, the platform loops are also to remain in use until the 1959 "power box" is demolished and the third platform line commissioned at the new station. This is expected to take place in spring 2016.