The results, based on responses from 716 charity chief executives, show that in organisations with turnovers of more than £25m, women are paid an average salary of £105,000, compared with £91,950 for men.
In charities with turnovers between £15m and £25m, women leaders earn an average of £78,817, compared with £76,650 for men.
In the sector as a whole, however, female bosses earn an average of £44,242, compared with £53,175 for men.
The report shows that although almost half of respondents took a pay cut to make the transition to a charity, voluntary sector salaries are becoming more competitive.
The average chief executive's salary for NGOs with a turnover of at least £25m is £94,000, just £16,000 less than the private sector's £110,000.
This compares with £78,000 and £93,000 respectively in 2000.
In charities with turnovers between £15m and £25m, the average salary is £78,300, up from £58,542 in 2000 - in the private sector it is £90,000, up from £78,500 in 2000.
The report shows that 47 per cent of chief executives previously worked in the public sector and 31 per cent in the private sector. Just over half moved because of an "interest in a specific job"; 44 per cent said they wanted to "make a difference".
Gail Scott-Spicer, deputy chief executive at Acevo, said: "It is striking that senior women in the major charities now earn more than their male counterparts. It's a world away from current practice in the commercial and public sectors. The competitive salaries we offer reflect the sector's growing professionalism. It's time to stop apologising for them."