The second phase of the project expanded opposite ends of the campus. A new science wing was built just north of the main building, while a new fine arts center was built just south of the old field house. A construction contract for both facilities was awarded to TAO Inc. of Bixby. Britt Embry of SPARKS of Tulsa was the lead architect, with the science wing handled by Barry Collier of SPARKS, while the fine arts center design was primarily by Keegan Jackson and Kirk Horner of The Hollis & Miller Group, Inc. of Kansas City.

Before this project, the science labs were split across two areas of the building and none of the labs met minimum state size standards. The new science wing cost about $2.5 million, or roughly 11% of the bond construction budget for BHS. The groundbreaking was on May 20, 2002 and the wing was dedicated on January 25, 2004. The 16,800 square foot wing houses two biology labs, three chemistry labs, and a physics lab. Each lab is about 1600 square feet with both lecture and lab areas, as well as an adjoining office/stockroom. There is a room for student science projects on one floor and a central chemistry stockroom on another. Each floor has student restrooms, and there are some small faculty restrooms.

Before this project, the school relied upon an auditorium that could only seat about half the student body and had never been remodeled since its construction in 1939. Cramped and obsolete fine arts classrooms were scattered across the campus. The new fine arts center consumed about $8.2 million in bond funds, or roughly 34% of the bond construction budget for BHS. The groundbreaking was on May 20, 2002 and the wing was dedicated on September 19, 2004. The 68,131 square foot facility features a 1200-seat auditorium, dressing rooms, as well as fine arts instruction rooms. There are rooms for choir, band, drama, stagecraft, visual arts, orchestra, and an arts computer technology lab. The last three areas are in the west end of the building, funded by a $1,000,000 donation from the Bartlesville Public Schools Foundation. The lobby of the fine arts center is shared with the new field house built just east of the center.