Farquhar was born in December 1979. He attended James Ruse Agricultural High School in Carlingford, NSW. He graduated from the University of New South Wales, with a Bachelor of Arts and Bachelor of Science.

Alongside his Business partner, Cannon-Brookes, Farquhar debuted on the 2007 BRW Young Rich list of the richest Australians aged 40 and under, and on the BRW Rich 200 in 2013 with an estimated net worth of A$250 million. In 2016, his net worth was estimated by Forbes on the list of Australia's 50 richest people as US$1.75 bn; by BRW Rich 200 as A$2.00 bn; and by the Sunday Times Rich List as GB£906 million.

With Cannon-Brookes, Farquhar is the co-founder and co-CEO of Atlassian, a collaboration software company that helps more than 51,000 large and small organizations – including some of the biggest names in media, Manufacturing and Technology – use Atlassian’s tracking, collaboration, communication, Service management and development products. He is also an adjunct professor at the University of New South Wales' School of Computer Science and Engineering. Cannon-Brookes and Farquhar were recognized for their achievements as the Australian IT Professional of the Year award in 2004, and Australian 2006 Entrepreneur of the Year. Farquhar has mentored through the Australian Businesswomen’s Network and gives guest lectures on entrepreneurship to MBA students and undergraduates.

He is married to Kim Jackson and they have three children. In 2017 Farquhar purchased from the Fairfax family its former ancestral Sydney harbourside home, Elaine, for approximately A$75 million. The Point Piper home set on 6,986 square metres (75,200 sq ft) had been in the ownership of the Fairfax family since 1891 and was vacant for nearly twenty years prior to its purchase by Farquhar.

In 2018, Farquhar spoke out about the Australian Governments changes after the 457 visas would be abolished, saying the move damages Australia's reputation as a place that people want to come to work.