In 1843 the Glasgow, Paisley, Kilmarnock and Ayr Railway opened to Kilmarnock [1st]. This location is where the passenger station (Kilmarnock [1st], to the north) and goods lines (Kilmarnock Goods, to the south) parted.
From 1847 it was the junction for the line to Troon. A new connecting line was opened going south west to meet the old, and rebuilt and regauged, Kilmarnock and Troon Railway. The connecting line crossed the approach to the goods yard on the level to reach Kilmarnock Junction, directly west of the station.
A locomotive shed opened north of the junction, with a carriage shed off to the east, north of Kilmarnock [1st].
The Kilmarnock Works (to the south south) and Kilmarnock Carriage Shed (north) opened in the 'V' of the junction.
The approach to Kilmarnock Goods was modified to be approached by a reversing spur on the south side of the Troon route.
In 1873 the Glasgow and Kilmarnock Joint Railway (joint Caledonian Railway and Glasgow and South Western Railway) connected to the junction from Kilmarnock Goods Junction to the north west. This was an incursion of the Caledonian into what had been entirely G&SWR territory. A separate Kilmarnock Joint Goods was to the north and approached from the joint line.
The station was rebuilt 1873-1878, resulting in today's Kilmarnock station. New signal boxes opened including a North box at the junction. This box was on the south side of the junction with the goods lines to its south.
It was replaced in 1890 with a new box called Kilmarnock No 1. This was renamed No 2 in 1926.
The original approach from Glasgow via Dalry Junction closed in 1973, although a long siding was retained as far as Crosshouse for civil engineers' use.
The joint line approach - the route which remains open north west of the station - was re-aligned. The high embankment between the Dalry and joint routes was removed and the joint route straightened (it formerly kinked to join the Dalry route). The original course of this survived as the reversing spur for J. Walker Kilmarnock.
The signal box closed in 1976, replaced by Kilmarnock Power Box which was built in the 'V' of the junction.