Huq was born in Hammersmith, west London to Sunni Muslim Bangladeshi parents who had emigrated to England in the 1960s. She grew up in Ealing, west London, with her two elder sisters, Rupa and Nutun. She was educated at Notting Hill & Ealing High School in London and left school with nine GCSEs and A-levels in physics, mathematics and chemistry. Huq studied sciences for her A-Levels, but chose to study economics at Robinson College, Cambridge and graduated from Cambridge University with a 2:1 degree.

In 1989, at the age of 14, Huq was a guest on Blue Peter with the National Youth Music Theatre, when she sang a solo. Before the 1992 general election, Huq interviewed Labour leader Neil Kinnock for the children's programme Newsround. She appeared as a contestant on Blockbusters in the same year. She also appeared as an uncredited extra playing a schoolgirl in the BBC One sitcom 2point4 Children in the Series 2 episode "I'm Going Slightly Mad".

Huq's presenting debut was in a GMTV Saturday morning children's quiz show entitled "Eat Your Words" between 1994 and 1996. She was assisted by Mark Speight before Simon Parkin took over. In 1997, several months before joining Blue Peter, Huq presented Channel Five's early morning children's programme Milkshake!, while also working as an editorial assistant for the now defunct Total Sport magazine.

Huq is best known for presenting the BBC children's television programme Blue Peter, which she joined on 1 December 1997. One of her most memorable early moments on Blue Peter was visiting Bangladesh, and speaking to members of her extended family whom she had not seen for many years. In the programme's 2004 "Summer Expedition" to India, Huq became an extra in the Bollywood film Musafir (2004), and practised dancing alongside its stars. For the programme's 2004 "Welcome Home" appeal, she made an emotional visit to Angola hoping to reunite children with their families (from which both had been separated due to war). In 2008, during her last programme, she broke a Guinness World Record by managing to pin 17 Blue Peter Badges onto fellow presenter Andy Akinwolere's shirt in a minute.

Between 2002 and 2004, Huq co-presented the CBBC Channel's UK Top 40.

In 2005, Huq took part in BBC One show Comic Relief Does Fame Academy. She was the third contestant to be voted off, after her rendition of Kim Wilde's Kids in America. She also travelled to Uganda and met orphan children, on behalf of Comic Relief.

On 15 September 2006, Huq became one of the presenters of The Tube with Tony Wilson, Alex James and Emily Rose on Channel 4 Radio working with production company UKoneFM. The first edition was broadcast on 3 November 2006. Huq made her debut as a news presenter on the BBC Asian Network in September 2007, in a series of documentaries on a radio current affairs programme called the Asian Network Report. In 2013, she took part in the Radio 4 series Great Lives, nominating Ada Lovelace.

In December 2007 Huq appeared on a Celebrity version of Ready Steady Cook with Blue Peter co-presenter Andy Akinwolere, and played a servant (also called Konnie, last name unknown) on the last episode of the second series of Robin Hood. Also in 2007, she began presenting the ITV1 London show London Talking, a political debate show, alongside Vanessa Feltz and Nick Ferrari.

In 2008 Huq travelled to Afghanistan with the charity Afghanaid to film a BBC Lifelines appeal, which was aired on 21 September. Huq was an ambassador for Gold Challenge, part of the official mass participation legacy programme for the London 2012 Olympic Games.

In December 2009 Huq won the Best Rising Star Screenplay Angel award at the Monaco International Film Festival for the short story Ahmed and Mildred. In March 2014 Ahmed and Mildred was selected to receive funding from Film London.

On 26 July 2010, Huq married satirist Charlie Brooker at the Little White Wedding Chapel in Las Vegas after a nine-month relationship. They have two children: Covey, born 23 March 2012, and Huxley, born 28 February 2014.

In February 2011 she appeared in an episode of the ITV2 documentary programme Under Pressure, where she attempted to learn how to be a Rapper. Trailers for the show asked "Will Konnie Huq it up?"

For two years running Huq has presented the Royal Shakespeare Company's Live from Stratford upon Avon – a web project aimed at showing theatre productions in schools. In July 2012 the project web-streamed a performance of I Cinna (The Poet). In November 2013 a recording of the Globe Theatre production of Richard II was shown in 3,000 schools. In both cases the performance was followed by a question-and-answer session hosted by Huq.

On 14 October 2014, Huq was one of the speakers celebrating Ada Lovelace Day at the Royal Institution.

On 29 June 2016, Huq hosted VOOM 2016 for Virgin Media Business’.