The display, which took place above the capital of Seoul, saw more than 300 drones take flight for a 10-minute show.
The drones displayed messages reminding people to wash their hands as well as thanking residents for staying safe.
The display, organised by the Ministry of Land, Infrastructure and Transport was intended to thank frontline healthcare workers, with a message saying "Thanks to you" flashing in the sky.
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The drones also formed a silhouette of the Korean peninsula alongside the message "Cheer up Republic of Korea".
The event was not advertised ahead of time so people did not crowd to view it.
Posting the video on YouTube, the government wrote: "Thank you for the efforts of the people and medical staff.
"We express our gratitude and respect to all who suffer from Covid-19."