The station is owned by Network Rail and managed by East Midlands Trains, who provide all rail services on the Nottingham to Skegness route.

Boston station was once an important junction, with two lines diverging in either direction. There was once 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.

Today, only the eastbound line to Skegness, and the westbound line towards Sleaford remain in use. Both surviving routes are single line, with a passing loop at the station, and operate roughly hourly. The seaside resort of Skegness is approximately 40 minutes away by train.