There are 4 main ways to deal with VAT on fuel.
Claim 100% of input tax: Only if you use the the car 100% business all the time eg a taxi firm. It is virtually impossible to have a car that has no private usage.
Claim 100% of input tax and pay the correct fuel scale charge: for your vehicle You can work out your fuel scale charge herehttps://www.gov.uk/fuel-scale-charge. This method can work out expensive unless the car does a lot of mileage and has low CO2 emissions.
Claim VAT just on business mileage: You will need to keep a detailed business mileage log and can claim 45p per mile in your accounts. This will allow you to claim back the VAT on fuel element of this rate using the advisory fuel rates, published here. You must make sure that you retain VAT receipts to show fuel purchased of at least the amount that you are reclaiming.
Claim no VAT at all: if you choose this option then you need to apply this across all the vehicles in your business, including commercial vehicles