Stephen Banham, who was out running with the club Team Balancise, heard cries from bin bags in a lay-by near Stanwick Lakes yesterday (Sunday) morning at about 8.30am.
It turned out to be a kitten that had been reported missing from Station Road, Burton Latimer, on Saturday night.
He said: "We were just running down and we heard this crying or something."
Stephen took to Facebook to describe what happened and said: "So this morning our long run was interrupted by the cries of a very distressed kitten.
"After looking we saw a bin bag moving on the other side of a ditch in the lay-by between Stanwick and Chowns Mill roundabout on the A45."
Speaking to the Northants Telegraph, Stephen said he had to climb across the ditch to get to the bag, so he thinks it was thrown.
He said the kitten was in two bin bags knotted at the top.
Stephen said: "We didn't know what we were going to find."
He said the kitten was in a "terrible" state and "didn't know what was going on".
Stephen also said he did not think the cat could have been in the bags overnight from when it was said to be missing, he said: "The cries it was making were really loud. It wasn't tired.
"I doubt very much it had been there since 10 o'clock the night before. I was working nights that night and it was really cold.
"It didn't seem like it had been there that long."
Stephen said his running club ran down the road around 10 minutes after another group had run the same way.
Stephen's club met with this group at Stanwick and none of them had heard the cries, making Stephen wonder if the cat had been left in that small window.
The kitten was taken to Northlands Vets in Kettering, where they recognised it as the missing kitten from Burton Latimer.
The little kitty was okay and has since been reunited with her owner, who posted an appeal on Facebook for her missing kitten at around 10pm on Saturday.
Stephen said Team Balancise choose lots of different routes and that the A45 is not a regular run for them, so it was very lucky they were there that morning and heard the cat.
A spokesman from Northamptonshire Police said: "This is obviously a very concerning incident and we are investigating it."