RURAL families in the region are paying an extra £1,500 a year for childcare compared to parents who live in urban areas, a report found.
A limited supply of nurseries and childminders is driving up costs for hard-pressed rural parents, according to the third NFU Mutual Countryside Living Index.
In the North-East, rural families are paying an extra £27 a week for childcare compared to households living in the region's town and cities, which equates to £1,508 more per year.
Rural residents in Yorkshire are paying an £16 extra per week - or £832 a year.
The report blames the price differential on supply and demand, with rural families having fewer available nurseries in their area.
According to the study, nearly a third of rural parents had just one nursery or crèche nearby and a quarter had none available within easy reach of their home.
Following recent changes to mortgage legislation, childcare costs will have to be factored into mortgage questionnaires, which could result in rural families facing tighter lending limits for home loans, the study claimed.
Liz Whitehead, 37, a mother of two from Leyburn, North Yorkshire, said families had limited options for childcare in her area.
She said: "There are very few to choose from and they are often full, although the ones we do have are usually very good.”
Tim Price, rural affairs specialist at NFU Mutual, said: “The lack of affordable, accessible child care in the countryside combined with sparse employment opportunities is making it it’s even harder for families to get by when they have young children.
“And with new mortgage rules meaning such expenses need to be factored into mortgage applications, this is another economic issue that young families living in the countryside face.
“However, while rural families do pay more for child care they also enjoy a high level of satisfaction with local education provision and a greater quality of life overall compared to their urban counterparts.”
The study revealed that rural inflation, which is based on a typical basket of goods consumed by countryside residents, had gone down for the first time since spring 2011.
A seven per cent drop in the cost of petrol and diesel and a 12 per cent fall in the cost of home fuels was found to be the driving force behind the one per cent drop in inflation.