The Czech Republic's Berdych, ranked seventh in the world, advanced with a 6-3, 6-2 decision over Latvian Ernests Gulbis at Ahoy Rotterdam.
He will be seeking his ninth career title but first since the 2012 event in Stockholm.
His opponent will be Croatia's Cilic, who bested Dutch wild card Igor Sijsling 5-7, 6-3, 6-2.
Cilic, coming off a victory at last week's PBZ Zagreb Indoors tournament, racked up his ninth straight win and will be going for his 11th career title.
Berdych owns a career 4-2 mark against Cilic.