The banks, which had previously been charging a £999 arrangement fee, said their focus was to offer competitive products which met the differing needs of their customers.
Andrew Pearce, retail director for Clydesdale, said: “As well as helping people to find the correct mortgage to suit their individual circumstances we are rewarding our existing customers with a no mortgage fee offer."
The arrangement fee will also be waived for new customers who are moving both their mortgage and current account to the banks.
Those just moving their mortgage from another lender will benefit from 50% off the arrangement fee.
In addition customers won’t have to pay any legal or valuation fees if they use Clydesdale and Yorkshire Banks’ appointed solicitors and valuers.
The mortgage fee offer is available on a range of fixed rate 2, 3 and 5-year mortgages as well as a number of offset mortgages.