In late 2009, Wellingborough was made a Penalty fare station by East Midlands Trains, which means a valid ticket or permit to travel must be shown when requested.

Much of this occurred when the branch to Higham Ferrers was built in 1894, when the up main platform was substantially altered, removing the original canopies.

2 Shed still exists, just to the north of the station at the far side of Mill Rd bridge; in 1966, it was no longer needed for railway purposes, and later became a warehouse for Whitworths and Totectors.

[4][5] On 2 September 1898, the station was the scene of a serious rail accident, when a trolley ran off the platform in front of a Manchester express train.

British Rail removed the fourth track between Kettering and Sharnbrook Junction in the 1980s, for cost cutting reasons, making platform 4 unused.

[9] As a wider part of the Network Rail upgrade, the Midland Main Line between Bedford and Corby has been electrified, with the fourth track reinstalled between Sharnbrook Junction and Kettering, which resulted in the rebuilding and opening of Wellingborough's platform 4 in 2021.

A station building on platform 4 is planned for access to the large Stanton Cross mixed-use development.

The replacement was built because of the Wellingborough East (Stanton Cross) development, as a new road bridge would start where the 'North' car park is situated and then go over the railway.