The snake, likely a runaway pet, had apparently been traveling through sewer pipes before popping up in the toilet.
"When I saw it I was pretty shocked,'' reptile catcher Chris Peberdy told the Northern Territory, after being called by a terrified resident. "It would certainly scare you if it came up from the depths of the toilet."
"There is no possible other way it could have got there than through the toilet. I had to give him a wash because he was wet and a bit smelly," Peberdy said.
Black-headed pythons are non-venomous species which are very rare in the Darwin area, but are popular in captivity.
Last October, a New York resident found a two-meter (7 foot) python in her toilet. While washing her hands at night, the woman turned round to see a python staring back at her from the toilet she had recently used.