The 29-year-old, who stormed to gold in the 100 and 200 metres at the 2004 and 2008 Games, became the first Japanese swimmer to qualify for four Olympics by breaking his own national record in the 100 earlier this week.
Kitajima eased up visibly over the last 25 metres in the 200 semi-finals to conserve energy for Friday's final, clocking two minutes 9.25 seconds behind Ryo Tateishi's 2:09.02.
"It's brutal," winced Kitajima. "There's nowhere to hide with these young swimmers. They don't make it easy for me. One more race to go and I need to rest up for it."
Kitajima, who obliterated his rivals in Athens and Beijing to complete the Olympic 100-200 double both times, had swam well within himself in the morning heats at Tokyo's Tatsumi Pool.
"I'm still feeling it a bit after the 100," admitted the former double world record holder. "I need to be even sharper for the 200 than I was for the 100."
Kitajima's national record stands at 2:07.51.
"Tomorrow I want to finish the job and make the team for the 200," he said. "I might have to break that record."