Due to adverse weather conditions that caused logistical issues, the start of the stage was delayed by about 15 minutes.
Heavy rain created huge puddles at the tiny start town of Lauwin Planque as the 182 riders set off on the 209km run towards the coastal port.
No less than one million spectators were believed to have lined the roadsides on the opening day of action, but the rain put a dampener on that kind of turnout on Sunday.
After Jasper Philipsen’s success on the first day of the race, Van der Poel powered to victory during an animated stage to continue Alpecin-Deceuninck’s dream start in the Tour de France 2025.
A large leading group stayed together for much of the stage, which boiled up into a mass sprint for the line, with Van der Poel edging out Pogacar in a photo finish and Denmark's Jonas Vingegaard taking third place.
"It was super difficult, the final was actually harder than I thought," Van der Poel said as he celebrated his team's second stage win in as many days.
"I was really motivated. It's been three or four years since I last won a stage (2021 - Ed.) so it was about time I got another one."
"People said I was a favourite for today, but if you see which riders were up there on the climbs, I think I did a really good job to be there."
Thanks to the win in Boulogne-sur-Mer, Mathieu van der Poel took over the yellow jersey in the general classification. Pogacar is four seconds behind the Dutch rider, while Vingegaard is third with a six-second deficit.
Monday’s stage of the Tour de France 2025 will challenge the peloton on a 178.3-kilometre ride in flat terrain from Valenciennes to Dunkerque, which seems to offer the pure sprinters in this year’s Tour a perfect chance to shine, so we're likely to see a mass sprint finish in the streets of Dunkerque.