Al Jazeera's Nicolas Haque reports from Dhaka, the capital, where over the past few years the government has been implementing a series of reforms to include more secular subjects in the curriculum and increase the numbers of female students.
The authorities have been offering incentives - providing cash to cover 80 per cent of scholastic costs - to see their reforms through.
This is proving to be hugely successful, bringing most madrassas under state supervision; religious schools that are largely funded by the government now follow both the state and religious curricula.
Zainul Abedine, the headmaster of the country's largest Islamic school, says: "In order to access government funds, many madrassas have opened their syllabus to other subjects like teaching languages such as English or Bengali. The number of madrassas have multiplied and so have the [numbers of] students".
With more then six million students currently enrolled, the madrassa system in Bangladesh is the second-largest in the world and is likely to get even larger as religious institutions open their doors to female students for the first time.
Maulana Abul Kalam Azad, a senior Islamic scholar, has welcomed the move to educate girls in madrassas.
"Girls are thriving – they tend to perform better than male students," he said.
A recent study by Nazmul Chaudhury, of the World Bank, found that young people's attitudes were interlinked with that of their teachers and that the presence of female instructors leads to increased openness in both female and male students.
In stark contrast to the allegations that madrassas cultivate intolerance, this study found that in Bangladesh "modernised religious education is associated with attitudes that are conducive to democracy".
Source: Al Jazeera (English)