"He's gone... Goku's gone!!"
In Age 766, Future Goku had been stricken down by a deadly Heart Virus that had no cure. Future Krillin, along with the other Z Fighters and company await the news of Future Goku's health outside Goku's house. However, Future Goku passes away, leaving Future Krillin without his best-friend. Six months later on May 12th, Age 767, the Androids attack and Future Krillin is killed by the Androids.
In the TV Special, Future Krillin is shown being attacked by Future Android 17 and Future Android 18, each shooting a Finger Beam at him at the same time. In Future Trunks' flashback in "Ghosts from Tomorrow", it is revealed that Krillin was blown up and killed by Android 17's Photon Flash.
Future Krillin was one of the last Z Fighters to die. He was 31 years old at the time of his death.
Dragon Ball Super
Although Future Krillin doesn't appear, his soul was destroyed when Future Zen-Oh erased the future multiverse to kill Zamasu once and for all.