There were cheers from the waiting crowds as she stepped onto the platform from the Royal Train, which was lined with hundreds of City of Culture volunteers.
The Queen, who is in the city to mark City of Culture year, was presented a posie of white rosies and rosemary from the gardens of Burton Agnes Hall by Islay Cunliffe-Lister, 11.
She smiled as she stopped to chat to some of the hundreds of people who had gathered at the railway station.
Evie Allen, 10, from Inglemire Lane, Hull, who there with her mum Naomi, said: "It's really good she is here, because she is 91.
"It must be really hard to travel and she has come all the way from London. She must have got up really early this morning."
She spoke to 11 people who have been involved in City of Culture Creative Communities projects, including artist Leonard Brown, who pointed out to her the full-scale replica of Amy Johnson's Gipsy Moth, which was built by prisoners from Hull Jail and is now hanging from the roof of Paragon Station.
The Queen, who was wearing an airforce blue cashmere coat by Stewart Parvin, and a hat with a diamond bow brooch by Rachel Trevor-Morgan, also spoke to head of Stepney Primary School Paul Browning, whose pupils have been involved in a project creating steel statues outside the former Stepney Station.
Mr Browning said: "She is just lovely. She exudes warmth, You often see her on TV and she looks a bit sombre but when you meet her she is just delightful.
"Our children are really enthusiastic about City of Culture. It has done a lot for raising aspirations and giving them a wider outlook.
"They have done lots of different projects including taking part in a Song for Hull."
The city has seen hundreds of cultural events since the year-long Hull 2017 celebrations began in January.
Hundreds of thousands of people have flocked to a huge variety of events which will culminate in the Turner Prize being awarded in the city next month.
One of the most high profile events of the year was Blade, in which a 250ft (75m) long wind turbine blade was installed in Queen Victoria Square.
The Queen visited the new Siemens factory and its state-of-the-art production line, where it was built.
She spent around half an hour in the factory and was given a tour of the production line and was shown a scheme aiming to encourage young people into engineering.
She also talked to apprentices including Charlie Fletcher, from Hessle, 20, and Chelsea Ward, 21, from Hull.
Miss Ward said: "She was lovely to speak to, very genuinely interested in what we had to say.
"She asked about the apprenticeships and if we enjoyed them and how long we had been here and if we enjoyed working for Siemens as a business."
The Queen finished her visit at the University of Hull, where she opened the Allam Medical Building, which is at the heart of the university's £28 million health campus.
Vice-chancellor Professor Susan Lea said: "It is a great honour to welcome Her Majesty The Queen to the University to open this truly outstanding facility.
"We are extremely proud of the vital contribution that our graduates and staff make to the health of the region and this investment enables us to extend our impact through the delivery of pioneering teaching and research."