The puppies were sitting in their own urine and faeces, about 230 metres (750 ft) from the RSPCA's Bryn-Y-Maen centre, in Upper Colwyn Bay.
They are believed to be three to four months old, and had been left with a saucepan and plastic bowl of water.
The charity said they "appeared healthy" but were nervous after their ordeal.
It is appealing for information, with calls treated in confidence.
Mike Pugh, RSPCA inspector, said: "It's so sad someone would think it acceptable to abandon two defenceless pups in a lay-by like this, and we're eagerly appealing to anyone with information to come forward.
"It is totally irresponsible to abandon pups in this way."
Dale Eccleston of Llwyn Landscapes, who found the puppies and looked after them, said: "I'm so passionate about dogs, and it was heartbreaking to see such young pups dumped like this.
"They were absolutely petrified, and I'm just so relieved we could help them."
Two puppies were found abandoned tethered to breeze blocks in a Conwy county lay-by, the RSPCA has said.