Clark was a regular starter for the first half of the season, but he didn't play a game after the February 4 fixture away to Crystal Palace.
The defender suffered a knee injury at Selhurst Park which would ultimately end his Premier League campaign.
"I had an injection a couple of weeks ago in my knee," Clark told the United's official website.
"Coming towards the end of the season, I'd been trying to train and doing a little bit outside, but it'd not been quite right, so we took the view that we'd leave it for a couple of weeks and hopefully it'll settle down.
"Hopefully, by pre-season, it'll be back to normal and I'll be ready to go again for next season."
Newcastle finished the season in 10th place after beating Chelsea on the final day of the season.
"It was a great end to the season," said Clark, signed from Aston Villa in the summer of 2016. "Everyone worked hard, and I feel like we got what we've deserved.
"I was injured for the last few games, but on the final day we could have finished between 10th and 15th and against Chelsea everyone would have backed us to drop a couple of places.
"But the lads put in a massive effort and, especially in the first half, that was probably the best performance I saw all season from us.
"We didn't let them have a sniff, really. They had a couple of chances in the second half, but the chances we created in the first half and the pressure we kept on them, they couldn't get out of their half – and they're a top side.
"We'll take a lot of confidence from that, especially going forward into the new season."