The British & Irish Lions scrum-half has not started for the new Scotland boss in his three games in charge of the team.
The Border Reivers player replaces Mike Blair of Edinburgh Gunners in the team.
Hadden has also switched his whole front row for the visit of the Samoans to Murrayfield.
Allan Jacobsen, Scott Lawson and Craig Smith move into the front of the scrum.
Stand-off Phil Godman is included on the bench but there is no place for Borders prop Bruce Douglas among the replacements.
Scotland were defeated 23-19 by Argentina in their first autumn Test on Saturday.
But Hadden insists his four changes to the team are not an indication of any displeasure with the performance at Murrayfield against the Pumas.
He said: "We set down to pick a team to win the match and we would never compromise on that aim.
"We have made changes because we want to show confidence in our squad.
"We have four really good players - the scrum-half and front row - who are worthy of an opportunity this weekend.
"In the front row, many clubs now rotate in that area and it is no reflection on performance of any player from last weekend."
Scotland team to play Samoa on Sunday:
C Paterson (Edinburgh Gunners); R Lamont (Glasgow Warriors), M di Rollo (Edinburgh Gunners), A Henderson (Glasgow Warriors), S Lamont (Northampton Saints); D Parks (Glasgow Warriors), C Cusiter (Border Reivers); A Jacobsen (Edinburgh Gunners), S Lawson (Glasgow Warriors), C Smith (Edinburgh Gunners), C Hamilton (Glasgow Warriors), S Murray (Edinburgh Gunners), J White (Sale Sharks), S Taylor (Edinburgh Gunners), A Hogg (Edinburgh Gunners).