Among the companies is a firm using artificial intelligence to monitor workplace behaviour and another running decoy computers to fool hackers.
They will have access to staff at the UK's most secretive agency and help bolster the country's online security.
The hub is in Cheltenham, but not inside GCHQ's doughnut-shaped complex.
The tie-ups could be a "twin-edged sword" for the agency, said Prof Anthony Glees, the director of the Buckingham University Centre for Security and Intelligence Studies.
"On the one hand the people at GCHQ work very hard to keep us safe from terrorists and increasingly, you hope, from hackers," he said.
Working with the private sector brought in new ideas, but "the other edge of the sword" was that it also came with security risks.
Although GCHQ had long worked with outside contractors, it would need to manage the risks of other firms having access to its staff and resources, he added.
A spokesman for the GCHQ Cyber Accelerator, which launched on Wednesday, suggested the agency was aware of the risks.
"All of the companies have been selected through a rigorous competition and have been subjected to appropriate background checks," he said.
The centre, which is in partnership with the government and telecoms firm Telefonica, also aims to boost the UK's Â£22bn cybersecurity sector.
"What GCHQ and the government recognise is that it's no longer just the big companies where you will find innovative ideas on cybersecurity," said Prof Alan Woodward, a cybersecurity expert at the University of Surrey.
Gloucester has long been a hub for defence contractors working with GCHQ, but the accelerator and the new National Cyber Security Centre are designed to attract new businesses to Cheltenham, he said.
The start-ups will be given a Â£5,000 grant each, access to government tenders and can work with GCHQ's network of international partners.
They include StatusToday, which uses AI to protect against insider attacks and detect mistakes, and CounterCraft, which defends large organisations through its deception platform.
The others are:
The UK's intelligence agency GCHQ is backing a new hub for tech start-ups in a rare glimpse into its approach to cybersecurity.