Princess Valkyrie (UFO Ultramaiden Valkyrie); via Key of Time
Homura Akemi (Puella Magi Madoka Magica)
Star Butterfly (Star vs. the Forces of Evil)
Misty (Super Doll Licca-chan)
Time Wizard (Yu-Gi-Oh!)
Aku (Samurai Jack)
Link (The Legend of Zelda: Breath of the Wild); via Stasis Rune
Lieselotte (Trinity Seven)
Bronze Dragons (World of Warcraft)
Eye of Agamotto (Marvel Cinematic Universe)
Wizards (Diablo 3) have the innate ability to cast several time-based spells.
Dimaria (Fairy Tail) in her Chronos form casting Age Scratch, a time-based spell that allows her enemy to regain all the injuries it sustained and healed up to the present point of time.
Ultear (Fairy Tail) is a prominent user of the Arc of Time, a magic that allows her to manipulate the time of objects, rewind time and enhance/strengthen people with powers gained from their own future.
Time Mages (Final Fantasy) are adept users of Time Magic, allowing them to slow, stop, or freeze enemies, fasten the speed of allies, manipulate gravity till a certain extent, and call upon the power of certain celestial objects to damage enemies.
Mages (World of Warcraft) through the Arcane school of Magic have the ability to cast spells like Time Warp.
Perse (Valkyrie Crusade) is an time mage.
Racer (Fairy Tail) making great use of his Slowing Magic, a time-effecting magic that alters the perception of time from his opponent's point of view
Morgana (Marvel) used magical time travel frequently.
Powered by one of the infinity stones, the Eye of Agamotto (Marvel Cinematic Universe) is a powerful magical artifact created by the sorcerer supreme Agamotto with the power to manipulate time.
...an artifact that Doctor Stephen Strange can wield with surprising skill.
Eclipse Gate (Fairy Tail), magic device invented by Zeref that allows people to travel through time.
Neo Eclipse (Fairy Tail) is immensely powerful spell that rewinds time on a massive scale, allowing restoration of persons past.
Tessai Tsukabishi (Bleach) using Forbidden Kidō spells to freeze time over a large area.
Hachigen Ushoda (Bleach) has invented unique space-time barrier spells.
Aku (Samurai Jack) uses a spell to open a time portal, sending Jack into the distant future.
Link (The Legend of Zelda: Breath of the Wild) can use Stasis to freeze objects in time.