The GWR was the first railway to serve the town with its line first from Taunton and then Castle Cary. The LSWR arrived from the east with its single line service commencing on 1st June 1860 into the GWR's first station at Hendford. The main line to Exeter, again initially single track, opened on 19th July 1860. Yeovil Town station - replacing Hendford - opened on 1st June 1861. The majority of LSWR trains came from the junction and the direct LSWR line from the east was lifted in the 1870s (although its earthworks can still be seen). Doubling of the LSWR main line was completed by July 1870. Earthworks, which also still exist, for a south west chord between the Clifton Maybank branch to the Weymouth line were constructed in 1860 but never used. In the late 1980s there was a proposal to finally lay track so that Weymouth services could call at the junction station involving a reversal, but these never came to fruition.

The original layout of the junction station had two island platforms with the through route taking the outer faces, encountering a severe 20 mph speed restriction in doing so, with a single track for the branch service to Yeovil Town between. For exchange of goods between the two railway companies the GWR built the Clifton Maybank branch, initially broad gauge, from the Weymouth line to a site to the immediately south of the LSWR's junction station.

Between 1907 and 1909 the junction station was extensively rebuilt, again with two island platforms but with four tracks between them, the centre pair being through tracks for non stopping services. The booking hall was, and still is, on the up island platform. The two platforms and the entrance to the station were linked by a lengthy roofed lattice footbridge.