The station has declined in importance since the 1960s. In its heyday the station employed over 50 staff and had two through tracks and cover over the platform tracks. The Skegness bound platform had classic Great Northern Railway architecture buildings as well, now replaced with plastic shelters. The station frontage remains, albeit altered, in partially reconstructed manner, and some of the buildings have found new uses.
Boston station was once an important junction, with two lines diverging in either direction. Today, only the eastbound line to Skegness, and the westbound line towards Sleaford remain in use. There was previously a southbound line to Spalding (closed in October 1970) that joined the line to Peterborough (and formed part of the original GNR main line from London to York), and a north-westbound line to Woodhall Junction (closed in June 1963) and thence on towards Lincoln, Horncastle, or Louth. Both surviving routes are single line, with a passing loop at the station.
To the south of the station the access to Boston Docks via the swing bridge and the site of the Broadfield Lane depot remain (the rail link into the docks still sees occasional use). To the north along the old Lincoln to Boston and Horncastle route, about 2 miles north of the town is the old Hall Hills sleeper depot.