The former Dawson's Creek star appeared alongside Gosselaar in last night's episode of Franklin & Bash.
However, he admitted that he is surprised that they have not worked together before.
"After years of being confused for one another, we actually met," Van Der Beek told Entertainment Weekly.
"I always thought we were the same person. It wasn't until I saw him on set that I realised we weren't."
Van Der Beek, who will star in ABC's new series Apartment 23, also revealed that he is pleased that he is getting more comedy roles and again credited his Funny or Die videos.
"The drama [offers] you expect, because that's what I've done before," he said. "But the comedies, getting offers for that, was a new experience and one I relish."
Apartment 23 will premiere on ABC in midseason and will air on Channel 4 in the UK.
> What Dawson Leery did next... 'Apartment 23'
Watch a trailer for Apartment 23 below: