English Pen was appealing against a commission decision of June 2007 to turn down its application amid concerns that its campaigning in support of human rights might constitute political activity.
The organisation also works to prevent poverty and to advance education. All of a charity's purposes must be charitable.
During its deliberations, the commission's board considered a previous court ruling that Amnesty could not be a charity because its object of "attempting to secure the release of prisoners of conscience" was political.
English Pen said its own letter-writing and campaigning activities were similar to Amnesty's, but argued that it conformed to the commission's recently-revised rule that political campaigning must not become a charity's "sole and continuing" activity because it accounted for only 20 per cent of its financial and voluntary resources.
The commission also noted that Amnesty tries to secure the release of prisoners "with or without the sanction of the local law", whereas English Pen "recognises that individual states may have legitimate reasons for limiting the exercise of human rights".
A spokesman for Amnesty International UK said: "It is a very welcome decision and, we hope, a promising sign." He said charitable status would save the organisation £1m a year.