Earlier this year, the Scottish SPCA accused the RSPCA of "stealing from the mouths of Scotland's defenceless animals" by running advertising campaigns in Scotland that did not make it clear that the charity does not operate north of the border.
According to the Scottish SPCA, 70 per cent of Scots are unaware the RSPCA operates only in England and Wales.
The RSPCA has agreed to include the phrase "the RSPCA helps animals in England and Wales" in prominent positions in all its newspaper and online adverts that are likely to be seen in Scotland.
It has also formally agreed to pass on any legacies made out to the "Scottish RSPCA" or the "RSPCA Scotland" to the Scottish SPCA unless there is evidence that this is not what the donor wanted.
Mark Watts, chief executive of the RSPCA, said he could not remember an occasion when a legacy had not been passed on, but admitted that the charity had inadvertently produced adverts in the past that had been seen in Scotland.
"We have formally recognised that there has been an issue about this," he said. "Having the memorandum will help to keep it in the forefront of the minds of people doing work on a day-to-day basis. It wasn't necessarily in the culture beforehand."
The memorandum was brokered by the Institute of Fundraising after negotiations hit an impasse.
Stuart Earley, chief executive of the Scottish SPCA, said: "There have been issues between the two charities for generations and we are therefore delighted to have reached agreement through the positive goodwill of all the parties concerned. There will undoubtedly be some teething problems, but there is a commitment from both charities to make this work."