Although last year's runner-up was unseeded, he was only behind Glen Durrant in the betting at 7/2 to lift the trophy and a warm favourite to see off BDO number one McGeeney.
A classy 110 checkout helped Noppert take the opening set before the Englishman turned on the style with a stunning 160 en route to storming through the second.
McGeeney whitewashed the Dutchman in the third set, managing a 120 checkout along the way, before edging the forth and fifth on deciding legs.
Both players had been tipped by our in-form darts expert in his pre-tournament preview so anyone who followed his selections have the advised 25/1 shot in the quarter-finals.
Earlier in the day, former world champion Scott Mitchell bowed out in a thrilling clash against Andy Baetens of Belgium.
The fourth seed, who averaged 96.39, came back from 2-0 down to level the match thanks to back-to-back checkouts of 121 and 141 but despite managing a 120 in the fourth set, Baetens edged a deciding leg to get his nose back in front before repeating the trick in the sixth.
Top seed Glen Durrant reminded everyone why he's favourite to retain his title as he averaged just short of 100 in a 4-1 victory over veteran Darryl Fitton during the evening session.
Former champion Scott Waites came through a thrilling clash with Dean Reynolds to triumph 4-2 with an average of 93.21 while Welshman Wayne Warren overcame Willem Mandigers of Holland 4-2.
In the women's competition, third seed Lorraine Winstanley is through to the quarter-finals after a 2-0 victory over Tricia Wright.
Wednesday results & Thursday schedule
Wednesday January 10
Afternoon Session
Second Round (Best of 7 sets)
- (13) Andy Baetens 4-2 Scott Mitchell (4)
- (3) Lorraine Winstanley 2-0 Tricia Wright (Best of 3 sets)
- Danny Noppert 1-4 Mark McGeeney (2)
Evening Session (7pm)
Second Round (Best of 7 sets)
- (10) Willem Mandigers 2-4 Wayne Warren
- (16) Darryl Fitton 1-4 Glen Durrant (1)
- (12) Dean Reynolds 2-4 Scott Waites
Thursday January 11
Afternoon Session (1pm)
Second Round (Best of 7 sets)
TV Coverage: Channel 4
- Justin van Tergouw v Killian Heffernan (Youth Final)
- Sharon Prins (8) v Deta Hedman (1) (best of 3 sets)
- Jim Williams (9) v Conan Whitehead
- Trina Gulliver v Aileen de Graaf (best of 3 sets)
Evening Session (7pm)
Second Round (Best of 7 sets)
TV Coverage: BT Sport
- Fallon Sherrock v Lisa Ashton (4) (best of 3 sets)
- Martin Phillips v Michael Unterbuchner
- Anastasia Dobromyslova (6) v Lorraine Winstanley (3) (best of 3 sets)
- Richard Veenstra (11) v Geert de Vos (6)
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