Time Spell Scroll (My Little Pony: Friendship is Magic)
Time Twirler (My Little Pony Equestria Girls)
Great Clock of Horologium Chamber (Little Witch Academia: Chamber of Time)
Tessai Tsukabishi (Bleach) using Forbidden Kidō spells to freeze time over a large area.
Hachigen Ushoda (Bleach) has invented unique space-time barrier spells.
Wizards (Diablo 3) have the innate ability to cast several time-based spells.
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
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.
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,...
...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.
Link (The Legend of Zelda: Breath of the Wild) can use Stasis to freeze objects in time.
Morgana (Marvel) used magical time travel frequently.
Powered by one of the infinity gems/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.
Starlight Glimmer (My Little Pony Series) uses Star Swirl the Bearded's time spell scroll to cast a spell to open a time portal over the Cutie Map to travel back in time.
The Time (Cardcaptor Sakura)
The Time-Turner (Harry Potter) contains the Hour-Reversal Charm.
Aku (Samurai Jack) uses a spell to open a time portal, sending Jack into the distant future.
Perse (Valkyrie Crusade) is an time mage.
Mages (World of Warcraft) through the Arcane school of Magic have the ability to cast spells like Time Warp.
Mallory (American Horror Story) is a witch gifted with Tempus Infinituum the power to travel through time and manipulate its flow.