The charge of Â£2 will begin on 28 July, but will only apply to goods costing less than Â£30.
The department store, which announced the move on Wednesday, said the current system was "unsustainable".
It said it handles six million click and collect orders a year, up from 350,000 in 2008 when the service began.
The charge will also apply to orders for collection at Waitrose, which is part of the John Lewis group.
A spokesperson for the company said that all click and collect orders were processed at distribution centres and then delivered to the designated shop, which incurred costs.
Last year, 18% of click and collect orders were less than Â£30.
Debenhams and Marks and Spencer said they have no plans to charge for their click and collect services.
John Lewis has said it will start charging to use its click and collect service, where customers buy goods online and pick them up in store.