South Kesteven District Council had the highest gender pay gap among Greater Lincolnshire authorities, government figures show.
The data shows women working for the council get 20% less money per hour than men.
This means that women earn around 80p for every £1 that men earn. Of those employees who earned the most at the council, 45% were women.
Councillor Helen Goral, Cabinet Member for Communications and Engagement, said: “South Kesteven District Council pays employees on the same grade the same amount, regardless of their gender.
“As our report demonstrates, the average hourly rate paid to men and women is also virtually the same, with just a 45p difference.
“The median rate is a more difficult measure to interpret and use to compare organisation to organisation.
“In SKDC’s case, the difference is partly due to the gender balance within certain teams, for example, our street care team consists of a large proportion of men, while the majority of our customer services team are women.”
Elsewhere, the City of Lincoln Council had a pay gap of 18% while 44% of the council’s top earners were women.
Angela Andrews, Chief Executive of City of Lincoln Council, said: “We are an equal opportunities employer and we ensure all our staff are treated fairly. We pay employees equally for the same roles, regardless of their gender.
“Any apparent pay gap is the result of the variety of jobs undertaken by men and women and the salary that these roles attract.
“We ensure our policies and procedures are fair and support a work-life balance for all. We also offer the opportunity for flexible working and monitor our workforce data to identify any trends and actions required.”
Meanwhile, Lincolnshire County Council had a pay gap of 13.3% with 55% of its highest paid staff being women.
South Holland District Council showed a pay gap of 16.5% and North Kesteven District Council had one of 4.3%.
But, both East Lindsey and West Lindsey District Councils submitted a pay gap of 10% and 22% higher for women than men.
This means that women earn £1.22 for every £1 that men earn at West Lindsey council.
North East Lincolnshire Council also had a higher rate for women with 8.3%, while North Lincolnshire Council had a 0.1% lower pay gap.
Boston Borough Council reported a pay gap of 0%.
It comes as companies and organisations are submitting their gender pay gap data to the government.
Firms with 250 employees or more are required to submit the difference in pay between male and female employees.