In a fractional reserve system, the commercial bank is allowed to loan out money in this way up to a set limit based on the amount of reserves they hold at the central bank. The interest rate of the central bank is the rate at which the central bank pays out interest on those reserves, not anything to do with the central bank lending money.
This paper sets everything out in detail: https://www.bankofengland.co.uk/-/media/boe/files/quarterly-...
EDIT: this explanation is the 'traditional' way, before central banks started doing QE. In QE, central banks purchase bonds and other assets, effectively 'lending' money out (the bond issuers will eventually, in theory, pay that money back). Still though, nobody is going to the central bank and borrowing money - the bank is buying assets (using money created from nothing, thereby increasing the money supply).