The vaulted basement, measuring approximately six metres by four and three-quarter metres, was built as a single unit with the Trim gate on its northern side, suggesting that the capacity to imprison people was considered a founding function of the castle rather than something added later. Its only entrance was a trapdoor from the floor above. There were no windows. Whatever daylight reached the first floor above the vault came through an entrance on the south-east wall facing into the castle ward; the basement itself received none at all. When excavation eventually cleared the space, a black deposit half a metre deep yielded pottery dating to the late thirteenth or early fourteenth century, and beneath it lay a flagged floor.

The written record of prisoners begins in 1294, with an escape of felons noted as early as 1300. What follows across the next two centuries reads less like a catalogue of common criminals than a register of medieval political misfortune. Hostages from Irish septs, including the O'Reilly and MacGeoghegan families, were held at Trim to guarantee the compliance of their kin, though it is unlikely they were confined to the dungeon itself. Those whose names survive in royal records tended to be prominent figures. Richard de Tuite, who had served as a Keeper of the Peace in the late 1320s, was incarcerated at Trim in 1344. In 1362, Art MacMurrough, king of Leinster, and his tániste (an Irish term for a designated successor or heir) both died at Trim under circumstances described as suspicious. Richard II used the castle to hold the future Henry V, and from 1390 seven hostages of Niall Óg O'Neill, including his son Brian, began what documents suggest was an extended stay. In 1402, all twenty-eight prisoners in the gaol escaped at once. Henry V, once free himself, later ordered the release of the Earl of Kildare, Sir Christopher Preston, and Sir John Bellew in 1418. In 1468, a prisoner named John Haddesore of Keppock murdered both the gaoler and his wife. By 1598, so many prisoners were being held that there was no court available to hear their cases.

The gaol outlasted the castle's period of active royal use by some margin, continuing to function even as the fabric of the building deteriorated under Tudor administration. Pardons were issued to under-gaolers in 1550 and again in 1558 following further escapes. Lease agreements from 1611 and 1624 included provisions for constructing a proper county gaol on the castle site, suggesting the existing structure was felt to be inadequate, though no replacement was ever built there. The court eventually relocated to the site of the old Franciscan friary around 1618, and by 1684 the gaol itself had moved to Mill Street.