"In Aleppo, Russia and the Syrian regime seek to make a desert and call it peace. The human tragedy is heartbreaking," he said.
Younger was the first serving MI6 chief to make such a public speech inside the agency's landmark headquarters on the south bank of the River Thames.
The speech was an attempt to open up a service that operates largely in the shadows, yet is accountable to taxpayers and is facing calls for greater transparency.
But the event was nevertheless restricted: a small group of reporters were picked up at a pre-arranged location in central London and taken to MI6 headquarters with nothing but a notepad to record the speech -- electronic devices were banned.
Addressing the reporters, Younger said that Russian and Syrian actions, in defiance of the international community, put the broader global fight against extremism at risk.
"I believe the Russian conduct in Syria, allied with that of (Bashar al-Assad's) discredited regime, will, if they do not change course, provide a tragic example of the perils of forfeiting legitimacy," he said.
"In defining as a terrorist anyone who opposes a brutal government, they alienate precisely that group that has to be on side if the extremists are to be defeated."
Younger, whose code name is "C" and who only writes in green pen, leads Britain's fight against terrorism around the world -- and the conflicts in Iraq and Syria are at the top of the list.
He said Britain cannot be safe from threats in the region unless the civil war in Syria is brought to an end -- "and brought to an end in a way that recognizes the interests of more than a minority of its people and their international backers."
How will Brexit, Trump affect security?
Younger also addressed concerns that European security could be at greater risk once the United Kingdom leaves the European Union and US President-elect Donald Trump enters the White House.
The UK works closely with French and German secret services and is America's closest intelligence-sharing partner.
UK agencies must work within domestic law. But during the presidential campaign, Trump touted the benefits of waterboarding, which is outlawed in Britain. President Barack Obama has banned these tactics, which are against international law.
Younger said he did not expect much change under the new US presidency and in a post-Brexit world.
"I'm often asked what effect the big political changes of 2016 -- Brexit and the US election result -- will have on these relationships," he said.
"My answer is that I will aim for, and expect, continuity. These relationships are long lasting, and the personal bonds between us are strong."
Threat of hybrid warfare
Younger also highlighted the "increasingly dangerous phenomenon of hybrid warfare," in what could be interpreted as a reference on Russia's alleged cyber interference
in last month's US election.
"The connectivity that is at the heart of globalisation can be exploited by States with hostile intent to further their aims deniably," he said. "They do this through means as varied as cyber-attacks, propaganda or subversion of democratic process."
MI6 must do what it can to uncover these activities and help the UK government and its allies defend against them, Younger said.
"The risks at stake are profound and represent a fundamental threat to our sovereignty; they should be a concern to all those who share democratic values."
Bond 'created powerful brand' for MI6
Younger is described as a career intelligence officer who led counterterror operations during the 2012 London Olympics. He has held various overseas postings, most notably as the ranking officer in Afghanistan.
Despite the whiff of James Bond about him, Younger said he was conflicted by the portrayal of the service in popular culture.
"Bond has created a powerful brand for MI6 -- as C, the real-life M -- there are few people who will not come to lunch if I invite them," he said.
But he said Bond -- or 007 -- wouldn't get a job in today's MI6. "For too long," said Younger, "people have felt that there is a certain single quality that defines an MI6 officer, be it an Oxbridge education or a proficiency in hand-to-hand combat.
"This is, of course, patently untrue. There is no standard MI6 officer. I need MI6 to have a workforce that harnesses the best talent regardless of background."