The Humboldt penguin scaled a wall and slipped though a fence at the Tokyo Sea Life Park in March.
It has since been spotted several times swimming in rivers running into Tokyo Bay, but had eluded keepers.
The fugitive penguin was finally recaptured on Thursday evening.
Two keepers went to a river after a sighting of the penguin was reported in the morning. They managed to catch it later that day on the river bank, a spokesman for Tokyo Sea Life Park said.
The penguin – known only as 337 – was being examined by experts but appeared to be in good condition.
“It hasn’t lost weight,” the spokesman said.
“It hasn’t got fatter either but its health seems good.”
After the penguin escaped, the aquarium launched an appeal for help and sent employees out searching.
On one occasion Japanese coast guards spotted the penguin and followed it but were unable to secure it.
Kazuhiro Sakamoto, vice-head of the aquarium, told Kyodo news agency he was “relieved to see the penguin come back alive”.
The penguin is one of 135 penguins at the park. Humboldt penguins breed on the Pacific coast of South America and offshore islands of Chile and Peru.
They are thought to be declining in number. One of the reasons is due to increasing water temperatures caused by the El Nino effect and reduced food supply.
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