It stated that Sudan's condition worsened significantly in the last 24 hours and he was unable to stand up as he was suffering a great deal.
"The veterinary team from the Dvůr Králové Zoo, Ol Pejeta and Kenya Wildlife Service made the decision to euthanise him".
At his death, there are only two females remaining alive and the hope that in-vitro fertilisation (IVF) techniques will advance enough to preserve the sub-species.
The plan is to use sperm from several northern white rhino males that is stored in Berlin, and eggs from Najin and Fatu and implant the embryo - which will be created in an Italian laboratory - in a surrogate southern white female, according to Ol Pejeta.
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The staff of Ol Pejeta Conservancy hope that, through "advanced cellular technologies" and IVF, his death will not signal the end of the species.
Efforts to save the species started in 2009 when the last four of the species, two males and two females, were moved to Ol Pejeta from Czech Republic. Last year, Sudan was listed as "The Most Eligible Bachelor in the World" on the dating app Tinder. One is his 27-year-old daughter, Najin, and the other is her 17-year-old daughter, Fatu.
The conservancy said Sudan's genetic material was collected on Monday.
Elodie Sampere, a representative for Ol Pejeta, said: "He was a gentle giant, his personality was just awesome and given his size, a lot of people were afraid of him. Throughout his existence, he significantly contributed to survival of his species as he sired two females", it said.
Northern white rhinos once roamed parts of Chad, Sudan, Uganda, Congo and Central African Republic, and were particularly vulnerable because of the armed conflicts that have swept the region over decades.
"They [northern white rhinos] used to be prolific across Northern Africa and have been reduced by poaching due to the demand of its horn", he said.