"Eternity can be a curse. It hasn't been easy for you, living without time. The losses you have had to suffer. A man can run out of things to live for. Lose his purpose, become a ronin, a samurai without a master. I can end your eternity, I can make you... mortal."
― Ichiro Yashida (The Wolverine)
"But i think the thing is the skull lord might actually be able to kill god tiers? Like bypass the whole judgment hullabeluga that makes em resurrect."
― Meenah talking about Lord English (Homestuck)
"You are the last of the deathless. The rest have been taken already. It is time for you all to finally rest."
Michael's Sacred Sword (Wishmaster 3: Beyond the Gates of Hell)
The Emoton Sword (Bravest Warriors) is the only way to deny the immortality of Emotion Lords and kill them.
Natsu Dragneel (Fairy Tail) Fire Dragon King Mode allows him to tap into Magic Power left to him by his deceased foster father Igneel to give him the ability to kill immortal beings such as Zeref.
When Zeref and Mavis shared a kiss (Fairy Tail) The Ankhseram's Curse stole just about all of Mavis' life force, which eventually killed her despite being immortal.
The Mortal Potion (Hercules) nullifies immortality.
SCP-4514 - The Thing That Kills You (SCP Foundation) is an anomalous switchblade capable of killing the immortal humans of the End of Death universe.
The Mortal Blade/Fushigiri (Sekiro: Shadows Die Twice) is an odachi that can permanently kill immortal beings such as Sekiro's sparring partner Hanbei the Undying, the Guardian/Headless Ape, the monks of Senpou Temple,...
...and even Sekiro himself in the Purification ending.
The immortal monster will long be haunted by the darkest spell of Moon the Undaunted (Star vs. The Forces of Evil)
The Star of Thundera's (ThunderCats) power is so great that it can totally negate the immortality of Mumm-Ra, the Ever-Living and kill him. Even a brief exposure to its full power left him near-death.
Gae Bolg (TYPE-MOON) is a cursed spear that inflicts wounds that do not heal until the spear is destroyed. And when it pierces the heart it divides into countless thorns that destroy the target's innards and deals damage scaled to the target's maximum HP.
Harpe (TYPE-MOON) is a monster-slaying holy sword that has a divine skill that nullifies the special abilities of immortals, negating their “undying” attribute. Wounds inflicted by Harpe can only be healed according to the laws of nature.
Gilgamesh (Valkyrie Crusade) is a murderous deity that kills other gods, being know as the god-slayer.
Lord English (Homestuck) can completely ignore a god tier's immortality, either by erasing them with his mouth lasers or with his canon-dissolving poison.