The world No 1 amateur fired an even par 72 at the Sebonack Golf Club to secure a top-40 finish. However the 16-year-old finished two shots behind fellow amateur Casie Cathrea of the US.
Ko ended the tournament at 11-over the card, tied for 36th.
World No 1 Inbee Park won her third major championship in a row. The South Korean finished four shots ahead of compatriot I.K Kim.
Ko didn't have the best start to her final round, recording bogeys on the fourth and sixth holes before regaining her composure to finish the front nine with three straight birdies for the first time this week.
A double-bogey at the par-four 14th saw her drop back to 12-over before she birdied the par-three 17th and record her second even-par round of the week.
