The 25-year-old Jumbo-Visma rider now has four wins for the season and will wear the Belgian tricolor for another year.
Van Aert beat World Hour Record holder Victor Campenaerts (NTT Pro Cycling) by 30 seconds over the 41.6km course, with Frederik Frison (Lotto Soudal) taking third with a time of 1:17.
"It was a mental advantage to start as the top favourite but you still have to finish it," said Van Aert after the race. "It wasn't easy.
"My plan was to have something left in the last lap, but in the end I was riding on character. Luckily with my fast start, I already had a lead.
"Of course you'd rather win with everyone present," he added, referring to the absent Remco Evenepoel. "But beating Victor is also beautiful."
Like Lotte Kopecky in the women's time trial on Thursday morning, Van Aert was in control of proceedings throughout the race, setting the fastest time at the first checkpoint on the course, situated in Koksijde's military base.
Campenaerts, in only his second race since the season restart, was 15 seconds down at the first check and couldn't recover over the rest of the course, shedding a further 11 seconds at the second checkpoint and 4 more by the finish.
Thomas De Gendt, another top time trialist hailing from the country, took his fourth fourth place at the event, fading after a strong start to finish 25 seconds down on his teammate in third. Frison had set the early running during the race, putting 40 seconds into another Lotto Soudal rider, Florian Vermeersch.
While Frison's effort was a strong one, the expectation was that Campenaerts and Van Aert would beat it, and so it played out on the pan-flat course.
Van Aert will now head to the Tour de France as domestique for GC contenders Primož Roglič and Tom Dumoulin, while also having his own chances.
Campenaerts, meanwhile, will look to continue Belgium's winning run at the European Championships next week. He won the title himself in 2017 and 2018.
The Belgian National Championships are split up this year, with the time trials held on August 20 while the road races will be held in Anzegem on September 22.
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Results
#
Rider Name (Country) Team
Result
1
Wout van Aert (Bel) Jumbo - Visma
0:50:10
2
Victor Campenaerts (Bel) NTT Pro Cycling
0:00:30
3
Frederik Frison (Bel) Lotto Soudal
0:01:17
4
Thomas De Gendt (Bel) Lotto Soudal
0:01:42
5
Florian Vermeersch (Bel) Lotto Soudal
0:01:58
6
Guillaume Seye (Bel) Beat Cycling Club
0:02:42
7
Senne Leysen (Bel) Alpecin - Fenix
0:03:24
8
Gilles De Wilde (Bel) Sport Vlaanderen - Baloise
0:03:28
9
Jasper De Plus (Bel) Circus - Wanty Gobert
0:03:29
10
Fabio Van den Bossche (Bel) Sport Vlaanderen - Baloise
0:03:42
11
Jonas Rickaert (Bel) Alpecin - Fenix
0:03:43
12
Xandro Meurisse (Bel) Circus - Wanty Gobert
0:03:50
13
Sasha Weemaes (Bel) Sport Vlaanderen - Baloise
0:06:13
14
Julien Van den Brande (Bel) Tarteletto - Isorex
0:06:21
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Dani Ostanek is Senior News Writer at Cyclingnews, joining in 2017 as a freelance contributor and later being hired full-time. Before joining the team, they had written for numerous major publications in the cycling world, including CyclingWeekly and Rouleur.
Dani has reported from the world's top races, including the Tour de France, Road World Championships, and the spring Classics. They have interviewed many of the sport's biggest stars, including Mathieu van der Poel, Demi Vollering, and Remco Evenepoel. Their favourite races are the Giro d'Italia, Strade Bianche and Paris-Roubaix.
