Bajaj Auto was established on 29 November 1945 as M/s Bachraj Trading Corporation Private Limited. It initially imported and sold two- and three-wheelers in India. In 1959, it obtained a license from the Government of India to manufacture two-wheelers and three-wheelers and obtained a licence from Piaggio to manufacture Vespa scooters in India. It became a public limited company in 1960.

With the launch of motorcycles in 1986, the company changed its branding from a scooter manufacturer to a two-wheeler manufacturer.

In 1984, Bajaj Auto signed a technical assistance agreement with Kawasaki, cooperating to expand production and sales of motorcycles in the local market.

In the early 2000s, Bajaj Auto bought a controlling stake in the Tempo Firodia company, renaming it "Bajaj Tempo". Germany's Daimler-Benz owned 16% of Bajaj Tempo, but Daimler sold their stake back to the Firodia group. It was agreed that Bajaj Tempo would gradually phase out the use of the "Tempo" brand name, as it still belonged to Mercedes-Benz. The name of the company was changed to Force Motors in 2005, dropping "Bajaj" as well as "Tempo", over the objections of Bajaj Auto with whom the company shares a long history as well as a compound wall.

In 2007, Bajaj Auto, through its Dutch subsidiary Bajaj Auto International Holding BV, purchased a 14.5% stake of Austrian rival KTM, gradually increasing its stake to a 48% non-controlling share by 2020. In December 2020, Bajaj started discussions on swapping its stake from KTM to KTM's controlling shareholder Pierer Mobility, a subsidiary of Pierer Industrie.

On 26 May 2008, Bajaj Auto Limited was split off into three corporate entities — Bajaj Finserv Limited (BFL), Bajaj Auto Ltd (BAL), and Bajaj Holdings and Investment Ltd (BHIL).

In 2017, Bajaj Auto and Triumph Motorcycles Ltd teamed up to build mid-capacity motorcycles.

In 2017, Bajaj and Kawasaki ended a sales and services partnership in India for the sale and after-sales service of Kawasaki motorcycles, which had been established in 2009. The partnership's dealerships were later converted into KTM ones. Bajaj and Kawasaki continue with their relationship in overseas markets.

On 26 November 2019, Bajaj Auto invested about ₹57 crore ($8 million) in bicycle and electric scooter rental startup Yulu. In this deal, Bajaj would also manufacture customised electric scooters for Yulu.