Alexander Pacteau, 21, is accused of killing Ms Buckley, whose body was found on Wednesday on a farm outside Glasgow.
Pacteau made no plea or declaration when he appeared at Glasgow Sheriff Court. He has been remanded in custody.
He is charged with murder and attempting to defeat the ends of justice.
Ms Buckley, 24, from Cork, vanished after spending the night with friends at Glasgow's Sanctuary nightclub.
She started an occupational therapy degree at Glasgow Caledonian University in February and was previously a nurse at the Princess Alexandra hospital in Harlow, Essex.
Earlier this week, her parents flew from Ireland to help with the search and told a news conference they were "desperate" for help.
Hundreds of people attended a mass at a church close to the Buckley family home in north Cork, and Irish foreign minister Charlie Flanagan said: "All of our thoughts and prayers are with Karen's parents, John and Marian, and with all of her family and friends at this tragic time."
A candle and photograph of Ms Buckley have been left at the reception to the health sciences building where she studied at the University of Limerick.
And tens of thousands of pounds have been donated to a fundraising page set up by Ms Buckley's former classmates to cover her family's expenses in Scotland.