Strachan has told the 30-year-old he will not be involved in the World Cup qualifier in Zagreb on June 7. McFadden won his 48th and most recent cap against Liechtenstein in September 2010, shortly before suffering a knee injury that kept him out for more than a year.
After frustrating spells with Everton and Sunderland, McFadden has rejuvenated his career at Motherwell since rejoining his first club in February.
McFadden has scored four goals in nine starts and shown evidence of the qualities that helped him strike 15 times for Scotland.
But he will have to wait until after the Croatia game to resurrect his international career.
"I've spoken to the manager and I won't be involved in that game," McFadden said. "He says I have missed a lot of football and he doesn't want to put too much pressure on me to play in the game.
"He wants me to get a good pre-season and maybe I'll come into the reckoning after that. He let me know if I was playing well I would be in consideration."
McFadden, whose future is uncertain beyond the end of the season, added: "I can understand where he's coming from but obviously at the same time I'm disappointed.
"I want to play as soon as I can. If he asked me to play now I'll be able to. But I take a lot from the fact the manager has phoned me and explained it to me.
"I can take that as a positive, get a good pre-season, work hard next season and try to impress him."