"Not guilty," the 45-year-old former close aide of Murdoch said as she appeared at Southwark Crown Court.
Several other former 'News of the World' (NoW) journalists, part of Rupert Murdoch's now-defunct Sunday tabloid in Britain, also appeared in the court.
Brooks also denied conspiracy to commit misconduct in public office and to pervert the course of justice.
Other NoW employees who pleaded not guilty to charges related to phone hacking included former assistant news editor James Weatherup and former managing editor Stuart Kuttner.
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The charges related to perverting the course of justice alleged that Brooks and her personal assistant, Cheryl Carter - who also denies the charge, tried to remove boxes of archived material from the News International archive between July 6 and 9, 2011.
In a second count, Brooks, her husband Charlie, former News International head of security Mark Hanna, security staff Lee Sandell and David Johnson, and driver Paul Edwards are all accused of conspiring to pervert the course of justice between July 15 and 19, 2011, by hiding documents, computers and other electronic equipment from officers investigating allegations of phone hacking and corruption of public officials relating to the two media titles.
The NoW's former royal editor, Clive Goodman, also appeared in court and denied two counts of conspiracy to commit misconduct in public office.
All the defendants were released on bail and are due to face trial later in the year.
The scandal led to a major Scotland Yard investigation when allegations emerged back in 2011.
Claims of wrongdoing have since spread to other papers outside the Murdoch empire, and a number of journalists, police officials, and executives have been arrested or dismissed from their jobs.