The name is readily assumed to derive from a crossroads where payments were collected from travellers entering the city, but the junction did not exist until modern times. In the 18th century a toll, appearing on maps as the Two-Penny Custom, existed at present-day Main Point, at the top of the slope emerging from the Grassmarket, where three centuries-old routes into the town from the West converged. The custom, introduced in 1680, was a tax on every pint of ale brewed outside the town walls. Main Point may therefore be the original Tollcross, the name being transferred later to the junction created when Lothian Road was laid in the 1780s. A milestone opposite Merchiston Castle in Colinton Road marked “1 mile from Tollcross” has clearly been measured from Main Point rather than the modern junction. The other toll in the area, dating from the 1755 Turnpike Act, was at the village of Wrightshouses, on the Wester Hiegait to Biggar (now Bruntsfield Place), roughly where the Barclay Church now stands. Its existence is recalled in the name of the nearby Auld Toll public house.

The earliest reference to Tollcross dates from 1439. The names tolcors, towcroce, tolcroce appear on 16th century maps, taking the form towcorse as late as 1787. It has been suggested that cros is a later form of cors (as in Old Welsh toll cors, meaning a boggy hollow) and that the ending -corse would have aptly described the low-lying area beside the now culverted Lochrin Burn running between the slopes of the Burgh Muir and the High Riggs south of the Grassmarket.