From 1984 through 1990, Siebel was an executive at Oracle Corporation, where he held a number of management positions. Siebel served as chief executive officer of Gain Technology, a multimedia software company that merged with Sybase in December 1992. Siebel was the founder, chairman, and chief executive officer of Siebel Systems, which was acquired by Oracle in January 2006. Siebel is the chairman of First Virtual Group, a Diversified holding company.

The Siebel Foundation (founded 1996) is active in support of the homeless and underprivileged, educational and research programs, methamphetamine abuse prevention, and alternative Energy solutions. The Siebel Foundation created the Siebel Scholars Foundation, the Siebel Energy Institute, the Dearborn Scholars Fund in Montana, and the Montana Meth Project. The Office of National Drug Control Policy awarded the Meth Project a White House commendation as the most influential prevention campaign in 2006, and Tom Siebel accepted the award on the program’s behalf. He was also recognized for his work on the program with the 2006 Director’s Community Leadership Award from the Federal Bureau of Investigation.

In 1999, 2000, and 2001, Fortune magazine recognized Siebel Systems as the fastest, third fastest, and second fastest growing company in the United States, respectively. The company earned other awards under Siebel’s leadership:

Call Center Magazine inducted Siebel to its Hall of Fame in 2000 in recognition for contributions to the Business and Technology of customer Service. CRM Magazine inducted him into its inaugural CRM Hall of Fame in 2003 in recognition of his vision, strong leadership, and enduring commitment to innovation. He has also been named:

In 2001, Siebel donated $32 million to his alma mater, the Department of Computer Science at the University of Illinois at Urbana-Champaign, to build the Siebel Center for Computer Science, opened in spring 2004. In 2006, Siebel donated $4 million to the University of Illinois at Urbana-Champaign to establish two endowed full professorships, the Thomas M. Siebel Chair in the History of Science and the Thomas M. Siebel Chair in Computer Science. Siebel pledged an additional $100 million gift to the University of Illinois at Urbana-Champaign in 2007.

Siebel received the David Packard Award for his achievements as a Technology Entrepreneur and his contributions to national security from the Business Executives for National Security in 2002 and was named one of the Top 25 Managers in the World by BusinessWeek in 2000 and 2001.

In 2005, Siebel founded the Montana Meth Project. Siebel continues to develop philanthropic initiatives.

In September 2008, Siebel hosted a campaign stop for Sarah Palin at his home.

On the morning of August 1, 2009, he and a guide were in Tanzania, observing a group of elephants from 200 yards away, when an elephant charged Siebel's guide and then turned on Siebel, breaking several ribs, goring him in the left leg, and crushing the right. They radioed for help, but it was three hours before he received any medical treatment. He was flown to the Aga Khan University Hospital in Nairobi, where they cleaned his wounds and stabilized his leg. He was then flown back to the United States on a 20-hour FLIGHT with only 10-hours of morphine and 15 hours of fluids. He had lost half of his fluids and was put in the intensive care unit. He was moved to Stanford Hospital where, over the next six months, they performed 11 surgeries, fixed his ribs and shoulder, and saved his left leg.

In September 2010, a year after the attack, Siebel had undergone 16 surgeries and an Ilizarov apparatus external fixator to mend, lengthen, and reshape the tibia of his right leg. After enduring 19 reconstructive surgeries total over two and a half years, Siebel has now made a full recovery. In 2013, National Geographic included Siebel’s account in its TV series Dead or Alive: Trampled on Safari

In 2013, C3 Energy hosted former Senator Max Baucus from Montana, and Siebel and Baucus discussed the ways in which information Technology addresses the utility industry’s big data challenge.

In April 2014, Congresswoman Jackie Speier from California met with C3 Energy executives, including Siebel, to discuss how the latest developments in IT are being applied to the power grid.

In 2015, Siebel founded the Siebel Energy Institute to research the data management of Energy infrastructure monitoring data. He is currently Chairman and CEO of C3 IoT.