The Family and Childcare Trust's latest annual childcare costs survey has found that some families pay £3000 more for a nursery place than in the cheaper council area next door.
Overall, the average cost for a child under two is said to be £5514 a year, rising for £8819 for 40 hours of care.
The report also found that childcare costs continue to weigh heavily on household budgets and are rising faster than inflation.
According to the charity's findings, nursery childcare for children under two is now 4.8% more expensive than last year, while the cost of a part-time place for two children is 22% higher than the average mortgage bill.
Finding childcare is also a major challenge for Scots, with fewer than one-quarter of Scottish local authorities providing enough childcare for working parents, compared to 54% in England.
The charity has called for tougher legislation for local authorities to provide sufficient childcare for children to tackle the serious gaps in Scotland's childcare provision, and a Government inquiry to examine the substantial variations in pricing between local authorities.
It also wants to see free early education made available to all two-year-olds and better use of school premises to provide high-quality and flexible childcare provision, particularly in rural areas.
Anand Shukla, chief executive of the Family and Childcare Trust said: "The high profile of childcare in Scotland reflects the challenges that families face today. Many families in Scotland desperately struggle to find childcare and if they do, they pay a sum similar to or more than a second mortgage for it.
"We warmly welcome the recent commitments on childcare from the main parties but setting out childcare strategies is only the first step.
"What matters for families is whether such policies mean that they will get the affordable, high-quality childcare that they and their children need."
Julian Foster, managing director at Computershare Voucher Services added: "Not only are costs in Scotland rising faster than in England, but Scottish parents also face a postcode lottery, with some quite staggering price differences between neighbouring local authorities, and there is clearly not enough childcare to meet Scotland's needs."
The Scottish Government has recently announced a raft of childcare measures, including giving an extra 8400 two-year-olds from families where no-one is in work 600 hours of free childcare from August.