Just step out of Naini Jn, there you'll find many e-rickshaws, rickshaws and autos, you can take them upto Leprosy Chauraha or upto Tikonia/Chungi depending on what mode of rickshaw you are in, the fare for Leprosy was 10 at for Tikonia was 20, not sure what's it now because last I travelled was about 10 months ago.

Or you can walk out of Naini Jn to Mewalal Bagia Chauraha which is hardly 200m or maybe 500m from there you can take Naini-Shantipuram electric bus and deboard at Tikonia, from Tikonia take...
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Shantipuram-Jhalwa Bus upto the church, you can tell them you want to go to Prayagraj Jn or Bada station they will guide you to deboard at opposite of Hotel Harsh from there you have to walk again 200/500m to reach Junction.
From Tikonia if you want to go to Civil Lines side of station you can take autos too, from Chungi to Hanuman Mandir and from Hanuman Mandir to Railway Station ₹20-₹20 each, you can argue for ₹10-₹10 too, but that depends how intimidating you can get.
For Platform 1 side or City side, deboard at Naini Chauraha also called Bangar Dharmashala Chauraha(100m early from Tikonia) and directly take a Vikram(the big bulky auto) upto the railway station for ₹20, they will demand 30 although