The space reopened last year after being closed for three years for refurbishment.
The musician said: “I have admired the beautiful work of Pierre et Gilles for years, their incredible portraits of icons like Jean Paul Gaultier and Marc Almond are truly iconic, and to sit for them was a dream come true.
“I was so happy when the National Portrait Gallery asked me if they could loan the piece.
“It’s very important to me to support the arts. Being in their new History Makers section is an honour.”
Smith, who uses the pronoun “they”, first found fame on the 2012 Disclosure song Latch and Naughty Boy’s 2013 track La La La.
They have gone on to achieve eight UK number one singles and three UK number one albums, including Gloria in 2023.