During a Joint Task Force Exercise (JTFEX) carried out in 1999, Boise was reported "sunk" by Dutch diesel-electric powered submarine HNLMS Walrus.

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.

[3] 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 Helena and Columbus.