The Canadian, 20, was beaten 6-3 6-0 on Saturday in what was the first Grand Slam final appearance of her career.
Despite failing to get her hands on the Venus Rosewater Dish, McEnroe believes that Bouchard will soon be among the silverware.
"Eugenie Bouchard has so many things to be proud of," he told BBC Sport. "Reaching the final was amazing for her and she will be back."
Kvitova's victory on Saturday saw the Czech win the title at SW19 for the second time in her career.