The Mullingar man was clear on the time sheets by 3.5 seconds from Adam McLean (Hanna Kawasaki) after lapping at 118.580mph on the KMR Kawasaki.
McGee, who finished as the runner-up in the Lightweight race at the Isle of Man TT, is aiming for a repeat of his victory in the class in 2015.
Dan Cooper was third quickest on Wednesday at Dundrod at 116.213mph ahead of Christian Elkin (115.280mph) and Dominic Herbertson (113.084mph).
Joey Thompson, riding the ILR/Mark Coverdale Paton, was seventh behind Jonathan Perry and Shaun Anderson on the Kramer 690.
Welshman Ian Lougher, back in action at Dundrod for the first time in five years, was 10th fastest (ILR/Mark Coverdale Paton).
McGee also led the way in the Ultra-Lightweight session on the Joey’s Bar Moto3 Honda (107.415mph) by 4.7s from Christian Elkin on Bob Wylie’s Honda, with Paul Robinson – a double winner last year – in third on the CB Racing Honda Moto3 machine. Chris Meyer was the top 125cc rider in fifth. Gary Dunlop was ninth on the Joey’s Bar 125cc Honda.
In the Lightweight class, Neil Kernohan was quickest at 108.813mph on the 250 Logan Honda from Stephen Morrison (400 Kawasaki), with Lee Johnston (106.697mph) third fastest on the Padgett’s Honda RS250. Gareth Keys (250 Yamaha) was fourth, clocking a speed of 104.170mph.