The 37-year-old had played 15 times for Town this season, and 33 times overall, but was first-choice until just five games ago when he lost his place to Mark Tyler.
Pilkington, who started his career at Manchester United, made over 140 appearances for County between 2005-10, and his appointment was announced by new Magpies manager Keith Curle on Tuesday.
Town boss Gary Brabin said: “It’s a great opportunity for Kevin and we wish him well.
“We’re obviously sad to see him leave because he’s been such an important member of the squad for the past few seasons - not only in terms of his performances on the pitch but his experience, know-how and character around the place.
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“Kevin has always been keen on taking up coaching full-time and he feels that this offer - at a club close to his heart - his ideal for him.
“On behalf of all the coaching staff and playing squad we’d like to wish Kevin good luck in his new role at Notts County.”
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