Younger was sponsored by the British Army through university. He was commissioned into the Royal Scots on 5 September 1986 as a second lieutenant. As a University Candidate he was a full-time student at university and trained in his spare time. On 10 December 1986, he transferred to the Scots Guards. On 16 June 1987, his commission was confirmed and dated to 5 September 1986; this signified the start of his full-time military service. He was granted seniority in the rank of second lieutenant from 9 April 1983. He was promoted to lieutenant, which was back dated to 5 September 1986, and was granted seniority from 9 April 1985. He was promoted to captain on 5 April 1989. On 10 April 1990, he transferred to the Regular Army Reserve of Officers, thereby ending his active military service.
Younger joined SIS in 1991. He joined the service at the same time as Richard Tomlinson, who in his book The Big Breach, portrayed him as 'Spencer', a St Andrews graduate and former Scots Guard who was recruited while working for the Halo Trust in Afghanistan. Younger served in the Middle East and Afghanistan. He became head of counter-intelligence in 2009, in which role he was involved in security for the London Olympics 2012. He became Deputy Director in 2012, before being nominated as Chief in October 2014. In a leaked list of 160 MI6 agents - which was originally believed to have been released by Richard Tomlinson, although government officials subsequently "acknowledged that the list did not come from Mr Tomlinson" - Alex Younger is mentioned as having been posted to Vienna in 1995. As of 2015, Younger was paid a salary of between £160,000 and £164,999 by SIS, making him one of the 328 most highly paid people in the British public sector at that time.
In 2016 Younger said cyber-attacks, propaganda and subversion from hostile states pose a fundamental threat to European democracies including the UK. In a rare speech by an MI6 chief while in office, Younger did not specifically name Russia, but left no doubt that this was the target of his remarks.
In December 2018, Younger raised concerns about Huawei's role in the UK's new 5G mobile network.
In December 2018 Younger gave a rare speech at the University of St Andrews, making emphasis of the need for fourth-generation espionage and fusing human skills with technical innovation. This was the second public speech in the four years since his appointment as "C" of the MI6. During the speech Younger addressed the case of Matthew Hedges, British university student who was arrested in Dubai and later convicted of being the Captain of British MI6, in which capacity he allegedly worked as an undercover agent in the UAE. Younger said he was perplexed by what has happened and that there are some frank conversations ahead between Britain and the UAE. Hedges was later pardoned by UAE President Khalifa bin Zayed Al Nahyan and reunited with his wife in the UK.
On 16 February 2019, when interviewed by the British press, Younger warned the British public about 19-year-old Jihadi Bride Shamima Begum who ran away to join the Islamic State in Syria in 2013 with two other religious Muslims including Amira Abase, and was heavily-pregnant with her third child. Younger told the press that people like Shamima are likely to have acquired the skills or connections that make them potentially very dangerous. Home Secretary Sajid Javid later chose to strip Shamima Begum of her British citizenship, leaving the future of her and her son unclear. Richard Barrett, who is a former director of global counter-terrorism at MI6, told the press that Begum should be given a chance to rebuild her life with her son. He also suggested it would be unreasonable to expect the Syrian Defence Force to look after her indefinitely. Barrett stated that British society should be strong enough to reabsorb her. He said the immediate reaction of the British government "has been a complete lack of concern for her plight".