Stones has faced criticism for his Premier League performances this season.
Stones' 2014-15 displays only enhanced his reputation as one of the nation's top centre-backs, and led to several big-money bids from Chelsea in the summer, the last of which was worth a potential £40million according to the Guardian.
However, Everton have failed to push on this season, with defence proving to be their Achilles heel.
Only five Premier League sides have conceded more goals than Roberto Martinez's side in 2015-16, and Stones was recently withdrawn from the Spaniard's starting lineup following criticism.
According to Gray, who played for Everton in the early 1980s, a spell on the sidelines could be beneficial for both Stones and England, and the Scot insists the 21-year-old will be a Three Lions player for years to come.
"Where John’s concerned, I’d play him, I really would," Gray told TalkSPORT's Alan Brazil Sports Breakfast show on Wednesday. "I think the guy is going to be a future England centre-back to come.
"He’s played enough games this year - he must have started 20 league games. It’s not like he’s not played at all.
"He’s fit, he’s a young guy, he’s 21 years of age, so it’s not a question about his fitness.
"We keep moaning (about) the fact that English sides, when they go to these tournaments at the end of the season, that all the best players have played too many games - well, you can’t say that about John.
"He’ll be fit, he should be ready, and I wouldn’t use that (a lack of games) as an excuse to not play John Stones."
Stones has started 22 of Everton's 29 league games this season - one fewer than his 2014-15 tally.