UK science will have to fight to make sure it is not an after-thought as Britain renegotiates its relationship with the EU, say research leaders.
The science establishment expressed its "disappointment" on Friday with the referendum's outcome.
It had been in the "remain" camp.
The decision to leave the EU now means new structures will have to be put in place if the science sector is to continue to enjoy favourable access to the union's programmes and funding.
Jo Johnson, the minister for universities and science - an "in" supporter - was one of the first to react.
He took to Twitter in the early hours to say: "Big decision. Let's make it work."
Britain's science sector has done increasingly well out of the EU in recent years, receiving €8.8bn in research funding in 2007-2013 versus the €5.4bn it paid in over the same period. And UK-based scientists have won about a fifth of all the grants, in terms of value, from the top-tier programmes run by the European Research Council.
This funding flow-back has been described as being akin to having another Research Council to go with the seven national bodies that presently distribute UK government monies.
To maintain access to the EU stream, Britain will likely now have to get itself some kind of "associated country" status, similar to the positions held by other non-EU countries such as Norway, Switzerland and Israel.
Associated countries pay a GDP membership fee to "join the club", after which, in principle, their scientists can bid for support in the same way as those from full EU member states.
But the exact arrangements will need to be worked out, and are going to depend on wider economic and political factors.
Switzerland, for example, only has "partial" associated status currently because it is not allowing Croatian citizens free access to its labour market.
And having free movement to work collaboratively is central to the way modern science is done.
Scientists for Britain is the group of researchers that has most prominently lobbied for Brexit.
It has argued that the policies of "political union" - and the regulations that flow from Brussels - are not a prerequisite for the UK playing a full role in European scientific collaborations.
The UK can survive and thrive outside full union membership, it contends.
And on Friday, its spokesman Dr Lee Upcraft said he was confident a new settlement would be found to maintain UK involvement in EU programmes and by extension the country's world-leading position in European and global science.
But he also urged the research establishment to hold government to account on national funding.
He echoed a recent complaint from Stephen Hawking, that "we've become reliant on EU funding. We get back a little more than we put in, and associated status will need to address this. But the other thing we need to do, and what UK academia needs to do, is get much better at lobbying government."
EU funding had masked a stagnation in national support, he told BBC News.
Dr Sarah Main from the neutral Campaign for Science and Engineering said there would inevitably be a big uncertainty factor going forward - which comes on top of sector changes already being pushed through parliament in the form of the Higher Education and Research bill (this will bring the seven Research Councils into a single body).
"In the run-up to the referendum, people talked a lot about associated status," she said. "To what extent the EU will make a clear path to enable the UK to obtain associated status and join science programmes back in the EU, I think will be driven by the politics.
"You have to remember that every associated country that people have quoted in the arguments up till now - none was previously a member of the EU that then exited. So, it won't necessarily be straightforward, but it would be welcome because we do want to compete in EU competitive funding streams, and as far as possible influence EU regulations, markets and the conditions for doing science and the training of scientists."
Prof Venki Ramakrishnan, the president of the Royal Society, agreed with Dr Main that ministers must not lose sight of science as they renegotiate Britain's relationship with the EU.
"In the upcoming negotiations, we must make sure that research, which is the bedrock of a sustainable economy, is not short-changed, and the government ensures that the overall funding level of science is maintained," he said in a statement.
Areas that should not be affected directly by the Brexit vote include the big intergovernmental research organisations.
The likes of the European Space agency; the European Southern Observatory, which operates major telescopes; and Cern, which runs the Large Hadron Collider - these are all separate legal entities to the EU.
However, EU money has increasingly been directed at some of their work. For example, Brussels is now the largest single contributor to Esa's budget, using the agency to procure the Galileo satellite navigation system and the Copernicus/Sentinel Earth observation constellation of satellites.
Britain's science-related companies working in these kinds of fields will want re-assurance that a renegotiated future does not turn into a competitive disadvantage.
Patrick Wood is the managing director of Surrey Satellite Technology Limited, which assembles the navigation payloads for every Galileo spacecraft.
He told BBC News on Friday: "We are days away from submitting the proposal for the next follow-on order, to complete the Galileo constellation, and we will continue to work hard with our supply chain to do this.
"I would look for our UK politicians to unite together to continue to support this flagship European project containing key UK technology, knowhow and to help protect jobs here in the UK."
Likewise, the chair of the House of Commons Science and Technology committee, Nicola Blackwood MP, wanted to highlight the care now needed to ensure the commercial science sector was properly supported.
"My committee's recent report into EU regulation of the life sciences pointed out that this sector alone comprises almost 5,000 companies employing 200,000 people in the UK, generating an annual turnover of £60bn. The Science and Technology Committee will want, in the coming weeks and months, to look at the consequences of this vote for British science," she said.