Brazilian forward Jesus has not featured since fracturing his metatarsal against Bournemouth on February 13.
But he has made rapid progress since rejoining the squad this month and will travel down to London ahead of the match.
Stones, however, is kept out with a muscular injury and is in a fitness race ahead of the derby next Thursday.
Guardiola said of Jesus: “(He’s) much, much better, today he made part of training with us. He’s is coming back with his happiness, and we are so happy. We are going to travel, all the group, to Wembley, he will be part of that and after that we’ll see.”
On Jesus’ impact since his arrival, Guardiola added: “The impact of Gabriel is shown by how difficult it is to come to the Premier League and have the effect he did.
“Against Tottenham, Swansea (you can see his impact). He had all Europe in his hands and he decided to come here, we cannot forget that. That’s why we are so happy that hopefully he can help us, along with Sergio and the others before the end of the season.”
The game is the third time City have faced Arsenal this season with two eventful Premier League encounters already completed.
City won 2-1 at the Etihad Stadium thanks to goals from Leroy Sane and Raheem Sterling, with Sane on target again in the 2-2 draw in north London.
The other man to score in that game was Sergio Aguero, who is on a blistering scoring streak of 11 from 11 games.
