The crime-reduction charity beat public-sector bodies and corporate giants such as IBM, which came fifth, PricewaterhouseCoopers (ninth) and BT (11th).
It is one of five third-sector organisations in the top 100. Citizens Advice was ranked 24th, the Skillset Sector Skills Council came 51st, the Shaw Trust was 94th and Barnardo's 97th. It is the sector's best performance since Stonewall started the index in 2005.
At Nacro, which came 5th last year, 98 per cent of gay male employees and 77 per cent of lesbian employees are out. This compares with an average of about 50 per cent for most organisations.
"We needed to improve our record on all aspects of equality to ensure that our services are accessible to all sections of the community," said Paul Cavadino, chief executive of Nacro.The fact that we have openly gay staff has encouraged gay service-users to come forward with their specific needs."
Cavadino said too many voluntary sector organisations were complacent about diversity and equality. "Equality doesn't just happen," he said. "If you don't monitor your organisation, you can fool yourself into believing you have good equality practice when you don't."
Stating a commitment to gay equality in job adverts and setting up a gay, lesbian and bisexual network had made the biggest difference to improving the organisation's record, he said.
David Shields, Stonewall's director of workplace programmes, said it was disappointing that only 19 of the 340 members of its Diversity Champions programme were from the voluntary sector.
More equal than others ...
2 Greater London Authority
3= Hampshire Constabulary
3= Staffordshire Police
6= Lloyds TSB
6= Manchester City Council
6= Transport for London
9= Brighton and Hove City Council