Aguero, who has scored 18 goals this season, has been left on the bench for the last two league matches as new signing Gabriel Jesus has been making all the headlines.
The 28-year-old Aguero is considered a legend at the Citizens, having scored 154 goals since joining the club in 2011 and playing a starring role as they have won all the domestic trophies on offer.
However, the Argentine's future at the Etihad Stadium has been a topic of discussion since Guardiola took over at the start of the season.
Asked if Aguero would at the club next season, Guardiola said: "At the end of the season I don't know. I know how difficult it is to find top goalscorers.
"I would like him to remain, but I don't know what is going to happen. Even in my career I didn't know what would happen at the end of the season."
The Spanish manager added: "Sergio knows the intention of his manager and the club. I don't want to sell him, I want him to stay here for a long time until he decides.
"The reason he's not played the last two games is because Leroy [Sane], Gabriel and Rash [Raheem Sterling] have played amazing. That's the only reason why. He remains a top player and an important one for us to achieve our goals. I don't have doubts about that."