Khan, who also owns NFL side Jacksonville Jaguars, has made an offer to the FA thought to be worth in the region of £900m.
Speaking to BBC Sport, Khan stressed that he understands fans' concerns over his offer for the 90,000-seat stadium, which is the largest in the United Kingdom.
"This offer makes a lot of sense for us," the 67-year-old said. "When I say us, I'm talking about the Jaguars, NFL, Wembley, and I think it also makes a lot of sense for the FA and the English football team. I'm pretty confident - that's why we're putting our name, our reputation on the line to get it done.
"I think [fans] have to understand the value and the attraction for myself. We'll leave the tradition and the stadium itself. Even though this is a new stadium, it does need upgrades. It means a lot to me because the first English stadium I went to was Wembley, and obviously it's iconic and historic and it means a lot to me.
"Under this arrangement the FA retains the right, the revenue, and that is really the most positive part of Wembley for the FA. So they will be retaining it and obviously we want it to be there."
Pakistan-born Khan has a current net worth of $7.2bn (£5.2bn) and is the 217th richest person in the world, according to the 2018 Forbes rich list.