Brisbane police said the 34-year-old man broke into the sex shop through the ceiling during the night, setting off an alarm inside.
The female owner confronted the thief, who threw sex toys at her and escaped back through the ceiling.
Police found the man on the roof and arrested him. On Sunday he was charged with breaking and entering, and drug offences.
It was the second rooftop break-in to sex shops within days in Queensland. In Cairns on Thursday, a 22-year-old man was charged with stealing a Fantasy Fetish pack which included a saddle.