The Malinois dogs had been missing since Thursday morning (January 28) after they escaped from a home in Regency Gardens, next to Euxton Balshaw Lane station.
An appeal went out on social media to help find them, with volunteers from across Chorley and South Ribble joining the search.
But on Sunday afternoon, a train driver passing through Euxton struck something on the tracks and reported his concerns to British Transport Police.
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Officers visited the scene where they found all three dogs had died on the tracks.
A spokesman for British Transport Police said: "Officers were called to the line in Euxton at 5.40pm on Sunday (January 31) following reports that a train had struck something on the track.
"Officers attended and very sadly three dogs were found dead. Their owner has been informed."