Jake Davis, 18, was charged with unauthorized computer access and conspiracy to carry out a distributed denial of service attack on the Serious Organized Crime Agency's website.
He faces five charges and is due to appear at Westminster Magistrates' Court on Monday, police said.
Police are investigating hacking groups known as Anonymous and LulzSec.
Officers from the police's Central e-Crime Unit arrested the teenager in what they describe as a "pre-planned intelligence-led operation" on Wednesday.
The UK Serious Organized Crime agency took its website offline for several hours on 20 June after it appeared to be a victim of a distributed denial of service (DDos) attack. LulzSec claimed responsibility for the attack.
DDoS is where large numbers of computers, under malicious control, overload their target with web requests.
Ryan Clarey, 19, of Wick ford, Essex, was charged last month with five offenses under the Criminal Law and Computer Misuse Acts, including an alleged hacking attack against Sosa's website.
LulzSec has previously also claimed responsibility for hacking attacks on the US Senate, Sony, the CIA and the Sun newspaper.
A 16-year-old boy from south London was arrested and bailed last week, while the international investigation has also led to sixteen arrests in the United States and four in the Netherlands.
Source: BBC News
Source: BBC News