The attendant was discovered dead in the Bungendore Road Caltex service station at 11.55pm by a colleague who was arriving for work.
Emergency services were called, but the man couldn't be saved and he died at the scene.
The slain man was a Pakistani student, The Australian reported.
His colleague arrived less than 10 minutes after the stabbing and came across "a gruesome scene," Monaro Police Superintendent Rod Smith said.
Police will allege the two boys walked into the Caltex store at 11.45pm and began fighting with the attendant.
"It's alleged during that struggle the attendant suffered a number of stab wounds which were fatal to that man," Supt Smith said.
Police launched an "intensive" hunt for the two boys, aged 15 and 16, who were captured by the station's CCTV cameras. It's believed the bloody attack was also caught on camera.
He wouldn't say if they were known to police, but both boys were from the Queanbeyan area.
The cash register and other items were taken from the store and significant damage was done when the boys had to "smash their way out" through a window after the door automatically locked behind them.
"Police allege they were involved in a number of other incidents in the Queanbeyan area. One being an aggravated break and enter where a man was bashed with a tyre iron, another where a man was bashed with a park here with a beer bottle."
The fifth incident was a stabbing of a man in Queanbeyan that has left the victim in a serious condition with a wound to the abdomen at Canberra Hospital.
A witness to that stabbing called police about 6.20am.
"It's alleged these two young people were involved in that."
About 15 minutes later police tried to pull over a silver Ford Falcon sedan and chased the car across the border into the ACT where the two teens were arrested without incident on the Monaro highway.
A weapon was found in the car, but it isn't known if it was used in the Caltex stabbing.
They are being spoken to by police where warrants and an extradition back to NSW are being prepared.
Police expect to lay a number of serious charges, Supt Smith said.
"Our investigation into these matters will continue, but it doesn't need to be said it doesn't get more serious than this - an absolute horrific series of events."
He wanted to reassure the public "two people we believe are involved in all of these are in custody."
Supt Smith said the Caltex incident appeared targeted in terms of "the location" but there was no known link between the arrested teens and the other victims.
A spokesman for Caltex told the ABC the company was vigilant about ensuring employees went home safely each day and provided a robust employee assistance program.
Caltex refused to say what after-hours security measures were in place at the station.