Thornton was eliminated at the first round stage of a World Championship for the first time in his career in 2016, when he could only take three legs off Alan Norris in a 3–0 defeat. He relinquished an 8–0 lead in the first round of the Masters to lose 10–9 against Dave Chisnall. On the opening night of the Premier League, Thornton averaged just 75.68 as Chisnall whitewashed him 7–0. He only won two matches out of 16 games to finish eighth in the table. Thornton was knocked out in the second round of the UK Open 6–4 by Arron Monk. Thornton suffered another heavy loss to Chisnall, this time 11–2 in the second round of the World Matchplay and he was beaten 2–1 in sets by Stephen Bunting in the opening round of the World Grand Prix. He lost in the first round of the European Championship 6–4 to Cristo Reyes and was involved in a nine dart shoot-out at the Grand Slam after Thornton and Dimitri Van den Bergh had both won two of their three games and were locked with a plus one leg difference. Thornton won by 345 points to 340 and then was defeated 10–5 by Michael van Gerwen in the second round. After losing 6–3 to Adrian Lewis in the first round of the Players Championship Finals, it meant Thornton had not progressed past the second round of any major event in 2016.