The LottoNL-Jumbo rider averaged over 51kph to head home teammate and European Time Trial Champion Victor Campenaerts by six seconds, with former World Time Trial Champion Vasil Kiryienka (Sky) a further second in arrears.
Boom now leads overall by eight-seconds from his teammate, with Kiryienka another second behind. Twelve riders lie within 30-seconds of the race lead, include Team Sky's duo Geraint Thomas and Owain Doull.
"I know, I always go out hard,” Boom said. "So I knew already in my mind that if it's headwind in the last few kilometres I'm going to drop some seconds, but in the end I could keep it on 45, 48 [kph], so it was quite OK and my team director was telling me that at one kilometre out I was still 10 seconds faster, so I knew it was OK."
Orica Scott's Luke Durbridge was the early leader, overtaking Harry Tanfield's (Bike Channel-Canyon) early pace setting time, before 2015 World Time Trial Champion Kiryienka went quicker with a time that home favourites Thomas and Alex Dowsett (Movistar) couldn't match.
Team Lotto NL Jumbo then took the lead with Campenaerts, before Boom usurped him going eighth from last, threatening to go under the 19-minute mark, finishing on 19min 2 sec. The Dutch team now hold three of the top five positions on General Classification, with Jos Van Emden fifth having scored the same position on the stage.
There was no change in the other classifications, with Elia Viviani leading the points and Jacob Scott the mountains.