The Soyuz rocket eventually lifted off at 5.01 am on Thursday carrying the Mikhailo Lomonosov research satellite and two small secondary payloads.
Speaking after the launch, Putin, said it could have been carried out on Wednesday, if it was not for the technology "trying too hard."
“They say that the proof of the pudding is in the eating, and to prove that a cosmodrome is ready for work you need to have a first launch. You made it and I congratulate you,” the President said.
“In 2007 we said we were going to have a complex like this and here it is. This is the first stage of a major effort and you have carried it out just fine,” Putin added.
The Soyuz rocket orbited Russia’s Aist-2D, Mikhailo Lomonosov and SamSat-218 research satellites.
Moscow University rector Viktor Sadovnichy said that the Mikhailo Lomonosov probe would contribute to the scientific study of particles reaching the earth from distant galaxies, powerful flares happening 500 kilometers above the surface of the earth, and keep an eye on the threats from asteroids and so-called “space junk” orbiting our planet.