Defender Coulton signed professional terms last summer and a second-year option on him has been triggered.
Amaral, a defensive midfielder, is reaching the end of the second year of his scholarship and he will stay on for next season.
Both players joined Aaron Bennett and Mikey O’Neill in training with the first-team squad at Euxton last week in the build-up to the Middlesbrough game.
Coulton, 19, who hails from Leyland, recently returned from a loan spell with Warrington Town and was on loan at Bamber Bridge before that.
The Scotland Under-19 international is left footed and can play at either left wing-back or in the centre of defence.
He was in the PNE side which beat Fleetwood Town 3-2 a fortnight ago to clinch the Central League North title.
Coulton is the only one of the four first-year professionals to have the option of a second year triggered, with Joe Rodwell-Grant, Jacob Holland-Wilkinson and Oliver Lombdard released.
Southport-based Amaral has been with PNE’s academy for a number of years.
His displays in the Under19s and reserves have caught Ryan Lowe’s eye, with him providing a physical presence in front of the back three.
Amaral is one of seven young players in the professional ranks together with O’Neill, Bennett, Harry Nevin, Josh Seary, Lewis Leigh and Noah Mawene.
Seary and Mawene will go into the second year of their scholarships in July but already have pro deals.
O’Neill, Bennett, Amaral, Nevin and Leigh are from the same age group.