But on Wednesday, Babchenko showed up at a news conference very much alive.
"We prevented the attempted murder of Babchenko by conducting a special operation", the SBU chief Vasily Hrytsak said at the conference before Babchenko came out, adding that the attempt on his life had been planned by Russian Federation for two months.
Kiev police chief Andriy Krischchenko said Babchenko's death could be linked to his "professional activities".
Mr Babchenko, 41, is one of Russia's best-known war reporters, but was forced to leave the country previous year because of repeated threats against him and his family.
Babchenko fought with the Russian army in Chechnya in the 1990s and went on to cover conflicts in Georgia's breakaway region of South Ossetia and Ukraine before leaving Moscow after a campaign of harassment a year ago.
Harlem Désir, the media freedom representative at the Organisation for Security and Cooperation in Europe, said he was "horrified" by Babchenko's death.
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Ukraine had released an image of a man wanted in connection with the killing. They said the killing may relate to his work.
Some even called for stripping Mr Babchenko of his Russian citizenship.
Police said the 41-year-old died of multiple gunshots wounds to his back.
"The Russian Investigative Committee is not going to ignore brutal crimes against Russian citizens", committee spokeswoman Svetlana Petrenko said.
Babchenko left Russian Federation after he criticized the Kremlin in a Facebook post in 2017.
In a controversial 2016 Facebook post, Babchenko wrote he had "no sympathy or pity" for the victims of a plane crash carrying Russia's Red Army choir to Syria given Moscow's support for Bashar al-Assad.
Vasyl Gritsak, head of Ukraine's security service, initially appeared at the conference before inviting Mr Babchenko to join him. "Like many dissidents I am used to abuse, but a recent campaign against me was so personal, so scary, that I was forced to flee".
He moved to Kiev last autumn, where he worked as a host for the Crimean Tatar TV station, ATR.
Babchenko served in the Russian army and fought during the first separatist war in Chechnya during the 1990s.