During a Joint Task Force Exercise (JTFEX) carried out in 1999, Boise was reported "sunk" by Dutch diesel-electric powered submarine . In the same exercise Walrus reportedly also took down eight other allied vessels, including the aircraft carrier and, flagship of the United States Sixth Fleet.
In 2002 Boise was assigned to the carrier strike group when the group took part in Operation Enduring Freedom.
In March 2003, Boise delivered some of the opening shots of Operation Iraqi Freedom when she launched a full load of Tomahawk missiles in support of the initial invasion. The ship and crew were later awarded the Navy Unit Commendation for their distinguished service in action.
In February 2017, Boise was no longer dive-certified as was awaiting scheduled maintenance at Norfolk. Due to congestion and delays in Navy shipyards, it was planned that Boise would receive maintenance at a private shipyard during Fiscal Year 2019. However, due to unforeseen delays she only entered drydock in early 2021. If she returns to service as scheduled in 2023, there would have been an eight-year pause between her patrols.[1]
The long wait has been attributed to a ten year lapse in capabilities and logistic setbacks discovered during the retrofit and restoration work done on submarines and .[2]