After Today ceased publication in 1995 he joined The Times, working as a news reporter on stories such as the Dunblane school massacre in Scotland, the death of Diana, Princess of Wales, in Paris and the conflict in Kosovo.

On 5 September 2009, while Farrell and his interpreter Sultan Munadi were in a village south of Kunduz, Afghanistan, investigating reports of civilian casualties in a NATO strike on two fuel tankers that had been hijacked by the Taliban they were kidnapped.

Corporal John Harrison, a British soldier from the 1st Battalion, The Parachute Regiment, Special Forces Support Group and Farrell's interpreter, Sultan Munadi were killed.

[11] Prior to his kidnap Farrell had ignored repeated warnings that it was too dangerous to travel to the site and was later criticized for his actions which cost the life of one of the soldiers involved in his rescue.

He was a member of the NYT video journalism unit which won an online 2013 National Edward R. Murrow Award for its breaking news coverage of the impact of Hurricane Sandy on New York.

[18] In 2016 he moved to the NYT's London bureau to work on the digital news desk, on the team developing a new design for the Times's website and mobile phone app.

In December 2017 Farrell joined Reuters news agency as a writer and video journalist and moved to Jerusalem as Bureau Chief for Israel and the Palestinian Territories, overseeing text, pictures and television.