Vladimir Markovnikov was born on December 22, 1837, in Chernorechye near Nizhny Novgorod, Russian Empire (now Dzerzhinsk, Nizhny Novgorod Oblast, Russian Federation). Soon after his birth, his father retired and settled in a family estate received as a dowry from his wife's family at marriage, in the village of Ivanovo, Knyagininsky district of the Nizhny Novgorod province, where Markovnikov spent his early childhood.
He joined the cameral department of the law faculty of Kazan Imperial University in 1856. He moved to the natural department of the university, where he attended the lectures of A. M. Butlerov. In 1860, after completing a university course, he was left to prepare for a professorship and was appointed laboratory assistant at a chemical laboratory. In 1864 he defended his master's thesis. In the spring of 1869, he defended his doctoral dissertation.