Kramer clocked six minutes, 10.76 seconds over the distance, with compatriots Jan Blokhuijsen claiming silver and Jorrit Bergsma the bronze to make it a Dutch clean sweep.
Kramer shaved almost four seconds off the Olympic record he set en route to winning the title at the 2010 Vancouver Games as he continued his unbeaten run over the distance this season.
He was nearly five seconds faster than Blokhuijsen on Saturday.
Poland's Jan Szymanski set the early pace in the second pairing before Russian fans were given something to cheer as Denis Yuskov went into the lead with a strong time in the seventh heat.
Kramer, benefiting from the ice being prepared just before his skate, trailed Yuskov's times before moving ahead of the Russian's mark with four laps remaining of the 10th heat.
Gritting his teeth, Kramer powered to the finish to set a mark that was always going to be incredibly difficult to beat and clenched his fists on crossing the line.
Blokhuijsen and Bergsma, skating in heats after Kramer, threatened the world record holder early before tiring over the final laps.
Vancouver games 10,000m champion Lee Seung-hoon of South Korea was expected to push Kramer but struggled in the 13th and final heat, finishing well down the field.
World record holder Kramer ran to the Dutch fans before throwing his winning bouquet of flowers to girlfriend Naomi van Aas, who won two golds with the Dutch field hockey team at the 2008 and 2012 Summer Games.
(Reporting by Patrick Johnston)
