The changes come into effect from 8pm today.
In its core range select products between 65 and 80 per cent LTV will rise by around 0.11 per cent.
On the product transfer side, certain products at 80 per cent LTV will be increased by around 0.04 per cent.
This includes its two-year fixed rate with £995 fee, which will be priced at 2.44 per cent. Its fee-saver equivalent will go up by 0.01 per cent to 2.69 per cent.
Its five-year fixed rate fee-saver product at the same LTV will go up by 0.04 per cent to 2.77 per cent.
The lender said that select exclusive purchase products will be withdrawn. This includes its two-year fixed rate at 75 per cent LTV with £495 fee, which had a rate of 2.49 per cent.
Its five-year fixed rate at 80 per cent LTV at 2.42 per cent will also be removed, along with its 85 per cent LTV equivalent at 2.53 per cent. Both come with a £495 fee.
Virgin Money is withdrawing its five-year fixed rate exclusive remortgage product at 2.3 per cent. It is subject to a £1,295 fee.