Shares in the company were down 3.8 per cent in early trading.
The firm reported 1.7 per cent growth in like-for-like sales in the first 18 weeks of the year, with growth driven by the local pubs estate. In its pub partners division, like-for-like net income was up 4.5 per cent after 16 weeks.
Greene King said it had made strong progress on the integration of Spirit, which it bought last year.
"As expected, uncertainty surrounding the UK's future withdrawal from the European Union has translated into a softening of some economic indicators and a reduction in consumer confidence," the company stated.
"While the broader implications remain unclear, a number of recent industry surveys have flagged risks to leisure spend and we are alert to a potentially tougher trading environment ahead."
The group's warning coincided with Wetherspoon's chair Tim Martin publishing a scathing criticism of Remain backers, comparing the upcoming Brexit negotiations with his own personal experiences as a pub boss.
Greene King also announced today that it has appointed former Tesco bigwig Gordon Fryett as a non-executive director. He will join the board on 1 December this year.
Philip Yea, chairman of Greene King, said: "I am delighted that Gordon has agreed to join our board. His extensive experience of retail and property will undoubtedly add value to our decisions as we develop Greene King over the coming years."