The change will take effect from May 2026, starting with pre-orders for Yoshi and the Mysterious Book.
According to Nintendo, the digital version of the game will cost £49.99, while the physical edition will be priced at £58.99 - a £9 difference.
In a statement, the company said: "Beginning in May 2026, and starting with pre-orders for Yoshi and the Mysterious Book, new Nintendo published digital titles exclusive to Nintendo Switch 2 will have an MSRP that is different from physical versions."
Nintendo stressed that both formats will offer identical gameplay experiences, with pricing differences reflecting production and distribution costs rather than content.
The company explained: "This change simply reflects the different costs associated with producing and distributing each format and offers players more choice in how they can buy and play Nintendo games."
The pricing shift will only apply to Nintendo-published titles, with third-party publishers and retailers still free to set their own prices.
Nintendo added: "As always, retail partners set their own prices for physical and digital games, and pricing for each title may vary."
It remains unclear whether the new pricing model will extend to existing Switch titles or previously released Switch 2 games, including Pokémon Pokopia.
The move reflects a broader trend across the industry, with companies such as Sony experimenting with flexible pricing strategies, including dynamic pricing on digital storefronts.
Nintendo’s approach marks a notable shift in how console games are priced, as the company looks to balance rising costs with evolving consumer buying habits.