The Harry Potter author, who lives in Edinburgh, has also spoken out about her views in a blog post, stating that independence "carries serious risks".
Her donation was received by the pro-union campaign "recently", Better Together said.
Writing on her website, Rowling said that, while she is "no fan of the current Westminster Government", she has concerns about the economic risks of independence.
"My hesitance at embracing independence has nothing to do with lack of belief in Scotland's remarkable people or its achievements," she wrote.
"The simple truth is that Scotland is subject to the same 21st century pressures as the rest of the world.
"It must compete in the same global markets, defend itself from the same threats and navigate what still feels like a fragile economic recovery.
"The more I listen to the Yes campaign, the more I worry about its minimisation and even denial of risks."
She continued: "The more I have read from a variety of independent and unbiased sources, the more I have come to the conclusion that, while independence might give us opportunities - any change brings opportunities - it also carries serious risks."
Referring to her donation to Better Together, she wrote: "I wanted to write this because I always prefer to explain in my own words why I am supporting a cause and it will be made public shortly that I've made a substantial donation to the Better Together campaign, which advocates keeping Scotland part of the United Kingdom."
JK Rowling's statement in full
Before you read the following, please be warned that it's probably of interest only to people who live in Scotland or the UK (and not all of them!) If you read on regardless, you need to know that there is going to be a referendum on 18th September on whether or not Scotland should leave the United Kingdom. If you're only vaguely interested, or pressed for time, there's a mention of Death Eaters in paragraph 5.
I came to the question of independence with an open mind and an awareness of the seriousness of what we are being asked to decide. This is not a general election, after which we can curse the result, bide our time and hope to get a better result in four years. Whatever Scotland decides, we will probably find ourselves justifying our choice to our grandchildren. I wanted to write this because I always prefer to explain in my own words why I am supporting a cause and it will be made public shortly that I've made a substantial donation to the Better Together Campaign, which advocates keeping Scotland part of the United Kingdom.
As everyone living in Scotland will know, we are currently being bombarded with contradictory figures and forecasts/warnings of catastrophe/promises of Utopia as the referendum approaches and I expect we will shortly be enjoying (for want of a better word) wall-to-wall coverage.
In the interests of full disclosure, I should say that I am friendly with individuals involved with both the Better Together Campaign and the Yes Campaign, so I know that there are intelligent, thoughtful people on both sides of this question. Indeed, I believe that intelligent, thoughtful people predominate.
However, I also know that there is a fringe of nationalists who like to demonise anyone who is not blindly and unquestionably pro-independence and I suspect, notwithstanding the fact that I've lived in Scotland for twenty-one years and plan to remain here for the rest of my life, that they might judge me 'insufficiently Scottish' to have a valid view. It is true that I was born in the West Country and grew up on the Welsh border and while I have Scottish blood on my mother's side, I also have English, French and Flemish ancestry. However, when people try to make this debate about the purity of your lineage, things start getting a little Death Eaterish for my taste. By residence, marriage, and out of gratitude for what this country has given me, my allegiance is wholly to Scotland and it is in that spirit that I have been listening to the months of arguments and counter-arguments.
On the one hand, the Yes campaign promises a fairer, greener, richer and more equal society if Scotland leaves the UK, and that sounds highly appealing. I'm no fan of the current Westminster government and I couldn't be happier that devolution has protected us from what is being done to health and education south of the border. I'm also frequently irritated by a London-centric media that can be careless and dismissive in its treatment of Scotland. On the other hand, I'm mindful of the fact that when RBS needed to be bailed out, membership of the union saved us from economic catastrophe and I worry about whether North Sea oil can, as we are told by the 'Yes' campaign, sustain and even improve Scotland's standard of living.
Some of the most pro-independence people I know think that Scotland need not be afraid of going it alone, because it will excel no matter what. This romantic outlook strikes a chord with me, because I happen to think that this country is exceptional, too. Scotland has punched above its weight in just about every field of endeavour you care to mention, pouring out world-class scientists, statesmen, economists, philanthropists, sportsmen, writers, musicians and indeed Westminster Prime Ministers in quantities you would expect from a far larger country.
My hesitance at embracing independence has nothing to do with lack of belief in Scotland's remarkable people or its achievements. The simple truth is that Scotland is subject to the same twenty-first century pressures as the rest of the world. It must compete in the same global markets, defend itself from the same threats and navigate what still feels like a fragile economic recovery. The more I listen to the Yes campaign, the more I worry about its minimisation and even denial of risks. Whenever the big issues are raised - our heavy reliance on oil revenue if we become independent, what currency we'll use, whether we'll get back into the EU - reasonable questions are drowned out by accusations of 'scaremongering.' Meanwhile, dramatically differing figures and predictions are being slapped in front of us by both campaigns, so that it becomes difficult to know what to believe.
I doubt I'm alone in trying to find as much impartial and non-partisan information as I can, especially regarding the economy. Of course, some will say that worrying about our economic prospects is poor-spirited, because those people take the view 'I'll be skint if I want to and Westminster can't tell me otherwise'. I'm afraid that's a form of 'patriotism' that I will never understand. It places higher importance on 'sticking it' to David Cameron, who will be long gone before the full consequences of independence are felt, than to looking after your own. It prefers the grand 'up yours' gesture to considering what you might be doing to the prospects of future generations.
The more I have read from a variety of independent and unbiased sources, the more I have come to the conclusion that while independence might give us opportunities - any change brings opportunities - it also carries serious risks. The Institute for Fiscal Studies concludes that Alex Salmond has underestimated the long-term impact of our ageing population and the fact that oil and gas reserves are being depleted. This view is also taken by the independent study 'Scotland's Choices: The Referendum and What Happens Afterwards' by Iain McLean, Jim Gallagher and Guy Lodge, which says that 'it would be a foolish Scottish government that planned future public expenditure on the basis of current tax receipts from North Sea oil and gas'.
My fears about the economy extend into an area in which I have a very personal interest: Scottish medical research. Having put a large amount of money into Multiple Sclerosis research here, I was worried to see an open letter from all five of Scotland's medical schools expressing 'grave concerns' that independence could jeopardise what is currently Scotland's world-class performance in this area. Fourteen professors put their names to this letter, which says that Alex Salmond's plans for a common research funding area are 'fraught with difficulty' and 'unlikely to come to fruition'. According to the professors who signed the letter, 'it is highly unlikely that the remaining UK would tolerate a situation in which an independent "competitor" country won more money than it contributed.' In this area, as in many others, I worry that Alex Salmond's ambition is outstripping his reach.
I've heard it said that 'we've got to leave, because they'll punish us if we don't', but my guess is that if we vote to stay, we will be in the heady position of the spouse who looked like walking out, but decided to give things one last go. All the major political parties are currently wooing us with offers of extra powers, keen to keep Scotland happy so that it does not hold an independence referendum every ten years and cause uncertainty and turmoil all over again. I doubt whether we will ever have been more popular, or in a better position to dictate terms, than if we vote to stay.
If we leave, though, there will be no going back. This separation will not be quick and clean: it will take microsurgery to disentangle three centuries of close interdependence, after which we will have to deal with three bitter neighbours. I doubt that an independent Scotland will be able to bank on its ex-partners' fond memories of the old relationship once we've left. The rest of the UK will have had no say in the biggest change to the Union in centuries, but will suffer the economic consequences. When Alex Salmond tells us that we can keep whatever we're particularly attached to - be it EU membership, the pound or the Queen, or insists that his preferred arrangements for monetary union or defence will be rubber-stamped by our ex-partners - he is talking about issues that Scotland will need, in every case, to negotiate. In the words of 'Scotland's Choices' 'Scotland will be very much the smaller partner seeking arrangements from the UK to meet its own needs, and may not be in a very powerful negotiating position.'
If the majority of people in Scotland want independence I truly hope that it is a resounding success. While a few of our fiercer nationalists might like to drive me forcibly over the border after reading this, I'd prefer to stay and contribute to a country that has given me more than I can easily express. It is because I love this country that I want it to thrive. Whatever the outcome of the referendum on 18th September, it will be a historic moment for Scotland. I just hope with all my heart that we never have cause to look back and feel that we made a historically bad mistake.