In Enniskillen, armed Williamite civilians drawn from the local Protestant population organised a formidable irregular military force.

The armed civilians of Enniskillen ignored an order from Robert Lundy that they should fall back to Derry and instead launched guerrilla attacks against the Jacobites.

The Jacobite dragoons under Anthony Hamilton stumbled into an ambush laid by Berry's men near Lisnaskea and were routed, taking 230 casualties.

Mountcashel managed to drive off Berry's cavalry with his main force but was then faced with the bulk of the Williamite strength under Wolseley.

The Cotter and Clare dragoons who rode away from the battle did not have significant losses, based on the October 1689 roll call.

The Williamite histories acknowledge that they captured approximately 400, including men who were later sent to Derry, which would indicate a total loss of killed, wounded, and missing of 800–900, and likely less.

The Williamite victory at Newtownbutler ensured that a landing by the Duke of Schomberg in County Down in August 1689 was unopposed.