The 60-year-old, who took over in December 2013, had to step away from his duties in December last year to undergo major heart surgery, and was replaced by interim boss Dean Saunders.
Former Aston Villa, Derby and QPR manager Gregory is still undergoing his recovery and watched from the stands as the club were relegated from League One this season.
Gregory said: “I would just like to take the opportunity to thank everyone at Crawley for their support over the last 18 months.
“Unfortunately I did not get the results on the field this season that I managed to get during the second half of 2013-14. Dean Saunders inherited the difficult task of trying to rescue our season with 24 games to go in January of this year.
“I would like to thank the board of directors in particular for standing by me and supporting me during the very difficult time I endured whilst undergoing open heart surgery. It was brilliant to see the stadium full for the last match of the season.
“I hope that the Crawley fans stand by their team and help to bring back the glory days again very soon.”
Crawley said: “The board of directors would like to place on record their sincere thanks to John for his efforts during his time in charge and his continued support of the club during his recent illness. He will always be a welcome visitor to the Checkatrade.com Stadium.”