Entering the 2016 World Championships in Boston as the defending champion, Fernández opened his short program with a quad toe loop-triple toe loop combination, then fell on his quad Salchow attempt, but recovered to complete a triple Axel, two level-four spins and level-four footwork, scoring 98.52 points and securing second place. After the short program, he could do little practice due to a recurring bursa on the heel of his right foot. On the day of the free skate, the medical team of the event attended to his injury for several hours and helped him to alleviate the problem. Fernández entered the free skate segment with a 12.04 deficit behind Yuzuru Hanyu – the largest point gap at the time between first and second place after the short program in any discipline at a World Championships or Olympic Games under the ISU judging system. Fernández completed a clean free skate, which included three quads (a toe loop and two Salchows, one in combination with a triple toe loop), two triple Axels, four more triples as well as difficult spins and level-four footwork, and scored 216.41, surpassing his personal best in the segment by 14.98 points. He reached a total score of 314.93, also a new personal best. His free skating and total scores were the second and third highest, respectively, under the ISU judging system as of the event. Hanyu made mistakes in his free skate, allowing Fernández to close the point gap and overtake him by a further 19.76 points to become the 2016 World champion.