Middlesbrough-born Hogg joined the Magpies from Ipswich Town as a lead player development coach but departs after just 18 months.
The club have announced the process to find Hogg’s replacement will begin “immediately”
Academy manager Steve Harper said: "This is a great opportunity for Chris to continue his coaching journey at a senior level.
"On behalf of our players and staff, I'd like to thank Chris for his efforts and extend my best wishes to him ahead of this next step in his career."
Hogg will join Manning, formerly of Belgian side Lommel, in the dugout on Saturday after they host Sunderland at the Stadium MK.
Newcastle’s young guns are due to kick-off their Premier League 2 campaign on Monday evening when they welcome Reading to Whitley Park.