The defender, who celebrated his 20th birthday on Sunday, penned fresh terms with the Reds to extend a stay that began when he joined the Academy as an U10 player.
Whelan – a Republic of Ireland youth international – switched to Merseyside from Crewe Alexandra, where he was coached by current Liverpool U23s manager Neil Critchley.
He was handed the captain’s armband for Critchley’s in-form side, who lead Premier League 2 by six points after a dozen games, at the beginning of the season.