Veterinarians on Monday used a chainsaw to cut off the horn of Pamir, a rare southern white male rhino.
"The risk that the rhinos currently face not only in the wild but even in zoos is too high and the safety of the animals is our first concern," said Premysl Rabas from the zoo in the central Czech town of Dvur Kralove nad Labem.
"The dehorned rhino is definitely a better option than the dead rhino," he added.
Veterinarians on Monday used a chainsaw to cut off the horn of Pamir, a rare southern white male rhino who was anaesthetized during the procedure.
"The intervention took less than one hour and it was performed without any complications," said Jiri Hruby, the zoo's rhino expert.
On March 7, the zoo in Thoiry near Paris said unknown intruders had broken security barriers and killed a male rhino of the critically endangered southern white subspecies for its horns.
The Dvur Kralove zoo currently has a herd of 21 black and southern white rhinos, including three calves who will not undergo surgery.
The cut horns are being stored in "an area outside the zoo" according to its spokeswoman, Andrea Jirousova, who added that they will likely soon be burned in public.
Black market rhino horn sells for up to $60,000 (56,400 euros) per kilo -- more than gold or cocaine -- with most demand from China and Vietnam where it is coveted as a traditional medicine and aphrodisiac.
Dvur Kralove is the world's only zoo to have succeeded in the captive breeding of the extremely rare northern white rhino.
In 2009, it placed three northern white rhinos -- one male and two females -- in the Ol Pejeta reserve in Kenya.
They are the last survivors of this subspecies, but they are not capable of breeding.
The zoo said last week experts would try to remove eggs from the two females at Ol Pejeta this year to save the subspecies by means of in-vitro fertilisation and embryo transfer to surrogate mothers.
The northern white rhinoceros has been nearly wiped out by hunting and poaching for their horns, and by wars in Africa, according to the World Wildlife Foundation.