Customers must now pay £1.99 to return products, with the cost deducted from their refund. The move, first reported by Retail Week, came into effect on 4 July.
Boohoo blamed the move on the rising cost of shipping.
High Street firms such as Uniqlo, Next and Zara already charge for online returns.
Online shopping boomed in the pandemic, but customers are more likely to return items bought online than in store, raising costs for retailers.
Analysts said other retailers were likely to follow suit in charging for returns.
"Shoppers have had an easy ride, but that's changing now - they will increasingly find there's a price to pay for returns," said Catherine Shuttleworth, retail expert and founder of Savvy Marketing.
"The costs, both financially and environmentally, have been stacking up for retailers... So retailers have been tightening up their returns policy by reducing the number of days a shopper can keep an item before expecting a return and in some cases charging a return fee," she added.
"We can expect to see this trend continuing and [now] we've seen Boohoo quietly introduce it. If you buy something for £10 at Boohoo, it's a real disincentive to return it if you lose £2, 20% of your investment to send it back."
Online shopping gained a lot of ground during the pandemic, with a big increase in the number of items being sent back.
For fashion retailers, returns can be costly. Not only do retailers often cover the costs of online returns as a way of winning customers from rivals, but it also takes longer for warehouse staff to process returned stock.
Many shoppers are also becoming more aware of the environmental impact of deliveries and returns.
In May, Boohoo said soaring returns were partly to blame for a slump in its annual profits.
It said customers had returned items faster than expected in the second half of the year, with the rate higher than it was before the pandemic.
Boohoo's brands include BoohooMan, Karen Millen, Nasty Gal, PrettyLittleThing, Coast, Misspap, Oasis, Warehouse, Burton, Wallis, Dorothy Perkins and Debenhams.
A spokesperson from Boohoo said: "As the cost of shipping has increased, we've had to look at where we can adapt without compromising what our customers love most, the convenience of shopping with us and the great value that our brands offer.
"This has meant that we will be applying a charge of £1.99 to returns so that we can continue to offer great prices and products and do this in a more sustainable way."