The charge of £2 will begin on 28 July, but will only apply to goods costing less than £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 £30.
Debenhams and Marks and Spencer said they have no plans to charge for their click and collect services.