The Netherlands international spent last season on loan at AC Milan, where he played 18 times under Fillipo Inzaghi and scored in the 2-1 home win over Roma in May.
Van Ginkel joined the Blues from Dutch side Vitesse Arnhem for around £8m in the summer of 2013 and made his debut in a 2-0 win over Hull.
But the 22-year-old is once again deemed surplus to requirements by Blues boss Jose Mourinho and now becomes the Potters’ fourth signing of the summer following the arrivals of Phillip Wollscheid, Jakob Haugaard and Joselu.
Van Ginkel will meet up with his new team-mates in Singapore ahead of their appearance alongside Premier League rivals Arsenal and Everton in next week’s Barclays Asia Trophy.
“Marco is the kind of player we have been looking to bring to the club,” Hughes told Stoke’s official website.
“He will bring great energy to the side and is capable of scoring goals from midfield, as he showed during his time with Vitesse.
“I’m looking forward to him linking up with the squad in Singapore and getting the chance to work with him on the training ground and see him in action in the Barclays Asia Trophy.”
Van Ginkel’s arrival at Stoke comes a day after Stoke sold midfielder Steven Nzonzi to Sevilla.