Lily the rabbit was spotted by a member of the public, who saw her on the roof of the two-storey building in Vanbrugh Road, Anfield, Liverpool, on Monday.
RSPCA animal welfare officer Matt Brown said she may have been stolen from a nearby house or "picked up by a bird from a garden".
He added it was "incredibly unlikely she'd have... hopped up herself".
Mr Brown said officers initially had "no idea where she came from".
"We knocked on doors on the street but we had no luck in finding her owner."
However, the RSPCA were later alerted to a Facebook post from Julie Galway, who lived nearby and was missing a white eight-month-old rabbit after someone broke into her garden on Sunday night.
Ms Galway said Lily had "definitely had an adventure".
"We'll never know for certain how she ended up on the roof, but thankfully she is fine and is back relaxing in her hutch."
A check by the vet found Lily was unharmed by her ordeal.
Merseyside Police confirmed there had been a report of a rabbit being stolen on Monday morning, which officers were investigating.
A pet rabbit which may have been thrown on a roof by thieves has been reunited with its owner after being rescued.