The retired Navy captain and 1986 academy graduate was chosen by the 219 graduating midshipmen as the most inspirational role model representing the academy's core values of courage in adversity, respect for others, integrity from within and service above all, federal officials said.
"Captain Kelly's life story is an inspiration to us all -- but especially for the midshipmen who are following in his footsteps as they graduate from the academy," U.S. Secretary of Transportation Ray LaHood said in a statement. "Personally and professionally, the example he sets does both the academy and our country proud."
Kelly is a best-selling author, prostate cancer survivor and veteran naval aviator who flew combat missions during the Gulf War.
The winner of many awards, including the Legion of Merit, two Defense Superior Service Medals and two Distinguished Flying Crosses, Kelly was selected as an astronaut in 1996.
He flew his first of four missions in 2001 aboard Space Shuttle Endeavour, which he commanded on its final flight in May 2011. He is one of only two people to have visited the International Space Station on four different occasions.
Kelly received international attention after the January 2011, assassination attempt on his wife. In their best-selling memoir, "Gabby," the couple shared their story of hope and resilience.
Giffords, who resigned her Arizona seat in January to focus on her rehabilitation, is expected to accompany Kelly at the June ceremony.
"Captain Kelly's impressive career as a Navy officer and astronaut along with his personal dedication and fortitude in the face of adversity makes him the ideal speaker to launch our graduates' careers as commissioned officers," said Shashi Kumar, the academy's acting superintendent.