With a runtime of 163 minutes, the extended version is the second longest animated film ever produced. After the extended version of In This Corner of the World (2016) with 168 minutes.

There are conflicting dates for the events in Final Yamato. Onscreen, the year is said to be 2203, but various sources for Space Battleship Yamato III claim that the events of Yamato III are set in 2205, two years after Final Yamato. No onscreen date is ever mentioned for Yamato III but Final Yamato does make references to the Bolar Wars from that series. Some speculate that Final Yamato's setting of 2203 was intended to retcon Yamato III out of continuity (due to that series' troubled production). Other's speculate that Yamato III may be set immediately after Be Forever Yamato (2202) and well into 2203, with Final Yamato being set late in that year.

Final Yamato was originally conceived as a fourth series, Space Battleship Yamato IV, which would have featured largely the same plot but with many additional twists; however, the real robot boom of the early 80's rendered the production of another romantic space opera inviable and the story was turned into a feature-length film instead.

The Dingirians are loosely based on Sumer, and they uses Sumerian words like Dingir, Lugal, and Uruk.

Shusei Nakamura developed a stomach ulcer and was unable to complete all of Daisuke Shima's lines. Isao Sasaki had to fill in for him for the missing dialogue.