Boris Chertok, a Russian rocket engineer who played a central role in designing the navigation systems for Soviet spacecraft during the race to the moon, among them the one that carried the first human into space, died Wednesday in Moscow. He was 99.

Russia’s state-controlled spacecraft manufacturer, RKK Energiya, for which Mr. Chertok was a consultant in his later years, said the cause was pneumonia.

For more than 20 years, Mr. Chertok was a deputy to Sergei Pavlovich Korolev, known as the father of the Soviet space program. Under Mr. Korolev, who died in 1966, Mr. Chertok was the primary designer of control systems for one of the world’s first intercontinental ballistic missiles, the R-7, and the Soviet Union’s earliest manned spacecraft, the Vostok, the Voskhod and the Soyuz.

“It’s difficult to think of any major event in the Soviet space program that he didn’t contribute to,” said Asif Siddiqi, a history professor at Fordham University and the chief translator of Mr. Chertok’s four-volume memoir, “Rockets and People,” published between 2004 and this year.