The Blues host the Gunners in the Premier League on September 22 - Sunday afternoon – then Watford on Tuesday evening barely 48 hours later.
With a crowded schedule, additional European matches and policing issues, the boss says it is inevitable these occasional fixture clashes will occur.
“It’s going to happen in many cases,” said Guardiola.
“Many times, [this will be] the situation for teams who play all competitions.
“The alternative was Thursday and if we’d been away in London it would have meant more days.
“We have a Saturday game against Newcastle, so of course to have more rest for Newcastle [is better].
“We play Tuesday because we can’t play Wednesday – Manchester United play in the Europa League and for the police it’s not acceptable [for two games in Manchester on the same night].
“It happened many times. It’s going to happen more and more and it is impossible to fix the calendar.
“It’s normal to happen. People say players and manager complain, but it’s about their health.
“Doctors say their bodies have to recover in four or five day, but more often it’s three then two.
“We will do our job, and we love to do it.
“Play the Champions League and then against Arsenal on Sunday.
“Not an easy game, then after two days later we have to do it. We prefer to play at home [then not have] to go to London.
“I decide to play on Tuesday because Thursday we have to recover for Newcastle.
“I’m not a specialist about the calendar. I’m not here to create the competitions and schedule.
“It’s not going to change - meetings are useless. They decide to do it.
“Tuesday we will be there. Hopefully we can select two teams. Everybody knows the schedule will be tight. In the end it won’t be a problem.
“I don’t know if we will have 20 players available. I don’t want to make Tuesday to try to play players who played Arsenal. Hopefully we can be fit.
“It’s not a physical rest, but mental. Stress and adrenaline and everything.
“Playing in front of many thousands people you want to play well.
“I said after the game against West Ham, the season starts this weekend - now the real season starts.
“We will see how we behave. Players recover quicker. We will see.”
