When Pennsylvania GovernorTom Ridge resigned on October 5, 2001 to become President Bush'sHomeland Security Advisor, Lt. Governor Mark Schweiker ascended to the governorship. By provision of the Pennsylvania Constitution of 1968, Jubelirer as President Pro Tempore was automatically elevated to Lt. Governor and sworn in the same day. Jubelirer's elevation to the office was not without controversy, as he retained his position in the Pennsylvania State Senate. Critics and political foes argued that this violated the separation of powers principle and threatened the checks and balances guaranteed in the state constitution. A lawsuit was filed by State Rep. John Lawless, Joseph Wiedemer and Leechburg Area School Board member Charles A. Pascal, Jr. to block Jubelirer's simultaneous service in the Senate and the executive branch, but the Pennsylvania State Supreme Court rejected the argument and issued a per curiam decision allowing Jubelirer to hold both offices simultaneously. Jubelirer continued in both offices until January 21, 2003 when Schweiker's term expired. He declined to accept the Lt. Governor's salary during his term. As Lt. Governor, Jubelirer served as President of the Senate, Chairman of the Board of Pardons, and Chairman of the Emergency Management Agency. In addition, he served as acting governor when Schweiker left the state. After his term as Lt. Governor expired, Jubelirer cosponsored a bipartisan bill in the state senate that would amend the state constitution and allow the Governor to choose a candidate to fill a mid-term vacancy in the Lt. Governor's office upon approval of the senate. The bill was not passed.
In May 2006, Jubelirer was defeated in the Republican primary by Blair County CommissionerJohn Eichelberger. He, along with Chip Brightbill, the Senate majority leader, were the first top-ranking Pennsylvania legislative leaders to lose a primary election since 1964. The defeat was attributed primarily to his role in drafting a legislative pay raise bill in July 2005. Jubelirer initially defended the raise. However, after internal polling showed his support falling, he opened discussion of a repeal of the unvouchered expense provision. However, newspapers reported that he tried to block efforts to repeal the entire raise. In the wake of the controversy, the Senator issued a statement in which he called the pay raise a "mistake"... I apologized for it in my district. I now think it was the wrong thing to do. Hindsight is 20-20. I'm not shifting the blame to anybody. I accept the responsibility." He pledged to return the money he had received from the unvouchered expense account. During the campaign, Jubelirer's more conservative challengers attacked him on abortion. Despite statements during the 2006 campaign that he was anti-abortion, Jubelirer's opposition to the Pennsylvania Abortion Control Act and a "pro-choice" rating by both the National Abortion Rights Action League and Planned Parenthood were used by opponents to counter his arguments. He told the Jewish Telegraphic Agency that he was "a pro-choice Republican" and that he did not support the Republican platform on abortion. Jubelirer's initial annual pension was $90,934.
Jubelirer attempted a comeback of sorts, seeking a seat on the Pennsylvania State University Board of Trustees. Despite an endorsement from former Gov. Tom Ridge, Jubelirer finished a distant sixth place, failing to earn one of the three seats. He was elected to The Pennsylvania State University Board of Trustees in 2014.
