Walker, 23, first thought he had signed permanently for the Iron in January. His free transfer move from Watford was blocked by Fifa regulations, meaning he instead had to join on loan.
As he had already played for the Hornets and Stevenage, he was only able to move to Glanford Park under "emergency loan" rules.
He made 18 appearances in that spell, scoring in last month's 4-1 win at Chesterfield, but is ineligible for the final three games of the campaign.
He said last week that he had turned down offers from elsewhere to commit his immediate future to the Iron, and his 12-month deal will come into effect from July 1.