Thapar had responsibility to turn around the BILT’s chemical division, which was suffering losses due to labour agitations and shortage of water and power. Gautam showed profits within a year, by scrapping the company’s expansion plans, selling off a few assets and dealing firmly with the labour. The family’s assets were divided into four in 1999, with Gautam’s older brother Karan parting ways in 2005. became the Chairman of Crompton Greaves on 22 July 2004.

When Lalit Mohan Thapar retired, he chose his nephew Gautam over Vikram. In 2005, Lalit Mohan handed over the reins of the business empire to Gautam along with his voting rights, shares and most of his personal effects in his will. Gautam became the Chairman of the Group on 1 July 2006.

He received the Ernst & Young Entrepreneur of the Year Award for Manufacturing in 2008.

Thapar is the President of Thapar University and former Chairman of the Ananta Aspen Centre. He is also on the Board of Governors of his alma mater, the Doon School. In 2010, he took over as the chairman of the board of governors of the Mumbai-based business school NITIE, for a 4-year period. He also promotes golf and is president of the Professional Golf Tour of India. The EUR 1.8m Avantha Masters, tri-sanctioned by the European Tour, the Asian Tour and the Professional Golf Tour of India, is India’s richest golf event and synonymous with professional international golf in India.

On 29 August 2019, he was sacked as Chairman of CG Power and Industrial Solutions with immediate effect after an investigation that unearthed a multi crore financial scam at the firm. On 20 August 2019, the company had stated that an investigation instituted by its board had found major governance and financial lapses in the company.