Tournament officials didn't provide a reason for Bouchard's decision to pull out of the Washington event. She hasn't played on tour since losing to Petra Kvitova in the final at Wimbledon on July 5.
Ranked No. 7 in the world, the 20-year-old from Westmount, Que., has made three previous appearances in the Washington event.
Wimbledon semifinalist Lucie Safarova will replace Bouchard as the Citi Open's top seed.