During a bedside hearing, the 29-year-old zoo worker was charged with one count of murder and refused bail.
Emergency services were called to the National Zoo and Aquarium in central Canberra about 12.50pm on Monday after people heard loud screams.
When ACT police arrived, they found a 29-year-old woman dead with stab wounds in a store room out the back of a commercial kitchen.
A knife was found at the scene.
The man was taken to hospital under police guard with self-inflicted wounds.
ACT Policing on Monday said it was unknown if the pair were in a relationship.
In a social media statement released on Monday night, representatives from the zoo said the menagerie would be closed on Tuesday following the "incredibly sad events", with operations to resume on Wednesday.
"The National Zoo and Aquarium experienced a tragic event on Monday involving staff members," the Facebook post read.
"We request that visitors and guests recognise the significant trauma that staff have experienced and that they respect their need for privacy on this matter.
"Our thoughts are with the families along with those staff affected in one way or another."
All zoo staff have been offered access to trauma counselling though police do not believe there is an ongoing threat to the public.
The man will next appear in court on April 4.
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