The pay gap between men and women working at the Department for Education (DfE) is 5.9%, new figures reveal.
The figure was calculated by how much an individual is paid per hour, so takes account of part-time workers.
The DfE is the first government department to publish the difference between the pay of men and women.
The national gap is 18.1%, but the DfE uses a different methodology so cannot be compared directly to the Office for National Statistics figure.
Education Secretary and Minister for Women and Equalities Justine Greening said her department was setting an example on promoting gender equality.
The DfE reported a mean pay gap - the difference between average salaries for men and women - of 5.3% and a median pay gap of 5.9%.
Pay gap data will be published by all government departments and large private companies by April 2018.
The ONS national gender pay gap for full and part-time workers is the lowest since records began in 1997.
Ms Greening said: "I'm proud that the DfE has taken an important step in reporting its gender pay gap, setting an example to other employers as we build a stronger economy where success is defined by talent, not gender or circumstance.
"The UK's gender pay gap is at a record low, but we are committed to closing it.
"As one of the UK's largest employers, the public sector has a vital role to play in leading the way to tackle the gender pay gap which is why the DfE's step to publish our gender pay gap matters."
The department says it has introduced a range of initiatives to support women in the workplace, such as supporting women returning to work, monitoring pay and helping women progress in their careers.