Upadhyay, an RSS ideologue was found dead in mysterious circumstances near the Mughalsarai station in February 1968.
The century-old railway station was painted Saffron at places and signboards with the new name were being put up ahead of the visit of the leaders.
The three leaders will flag off a passenger train and a goods train with an all-woman crew, and also launch a smart yard project at the century-old station on the busy Delhi-Howrah route.
Railway officials said it will be the first time in the country that an all-woman crew runs a goods train.
The leaders will launch a project to upgrade the yard at the station, officials said.
Ekatmata Express, now set to follow a new route from Lucknow to Mughalsarai, will get the green signal.
Union Minister of State for Railways Manoj Sinha, UP Deputy Chief Minister Keshav Prasad Maurya and other senior BJP leaders will also be present.
On paper, Mughalsarai station got a new name after Uttar Pradesh Governor Ram Naik gave his assent to the proposal in June.
The Centre gave its in-principle approval last year to the state government's proposal to rename the station, which is among the busiest in the country.
(with inputs from PTI)