Crews arrived at New Brighton marine lake in Wirral, Merseyside, at 03:15 BST after reports a boat had been taken without permission.
By the time the coastguard, police and firefighters reached the area about 10 minutes later, the youths had left.
The abandoned boat was found drifting.
The youths had left it in the middle of the marina, the coastguard said.
They had been apparently playing the augmented reality game and attempting to "follow" one of the characters across the lake.
Since the game's launch, its popularity has prompted a series of safety warnings and reports of players finding themselves in dangerous situations.
On Monday, a caller dialled 999 to report a 'stolen' Pokemon in Gloucestershire.
Senior North West coastal operations officer Danny Jamson said: "We know that many people are enjoying Pokemon Go across the UK and we wouldn't want to spoil that fun.
"However, we would ask people to use a little common sense and not to take risks while looking for Pokemon.
"The incident this morning shows that risk-taking can put not only you in danger, but also the rescue services who have to come to your aid."
A coastguard was called into action when a group of Pokemon Go fans tried to row across a lake in a bid to "catch" one of the virtual reality characters.