Professor Cath Noakes,and Professor Sheena Radford have been awarded OBEs in this year's list.
Dr Linda Pollard, who is the chair of Leeds Teaching Hospitals NHS Trust and was the Pro-Chancellor for the university for six years, has been made a Dame.
Cath Noakes, Professor of Environmental Engineering for Buildings, has been given an OBE for services to the COVID-19 response.
She said she is "delighted" and hopes the award demonstrates to young women that engineering is a "deeply rewarding profession.”
Professor Noakes said: “I am absolutely delighted to have been given an OBE. Without a doubt, the last few months have been extremely hectic.
"I am amazed at the amount of knowledge that we have been able to develop about a new pathogen. It demonstrates the power of scientific collaboration – and the role that engineers play in keeping people safe.
“I also want this award to demonstrate to young people – and particularly young women who are under- represented in the profession – that engineering is a deeply rewarding profession.”
Professor Noakes’ research team at Leeds has developed models to simulate the spread of pathogens inside buildings and other enclosed spaces, how surfaces can become contaminated, and the role of ventilation, air-filtration and disinfection systems in reducing those risks.
Professor Sheena Radford, the Director of the Astbury Centre for Structural Molecular Biology, has been honoured with an OBE for her research at the frontiers of molecular biology.
As director of the Astbury Centre for Structural Molecular Biology, Professor Radford has led a large group of researchers investigating the complex molecular basis of life.
Research in the Centre is fundamental to the big challenges facing society, including understanding diseases associated with ageing, how to improve cancer therapies and tackle antimicrobial resistance.
She said: “I am thrilled to be named in the Honours List. Although I may be the recipient of the honour, it reflects the hard work and dedication of all of the researchers in my team and in the Astbury Centre.
“We are bringing people together from the different branches of science to work on some of the big, unsolved problems in science.
"The progress we are making is only possible because of the team spirit and culture of collaboration that makes coming to work each day a joy.”
Dr Linda Pollard has been honoured for her services to healthcare and the community.
She has been involved in a major overhaul of healthcare in Leeds including the development of two new hospitals that will advance the NHS’s research work.
Dr Pollard said: “I am absolutely convinced about the benefits that research and innovation will bring to the city and the wider region.
"That’s why I have tried to play my part in encouraging, supporting and leading collaboration between key institutions in the city, including the NHS, the University of Leeds, and Leeds City Council.
"We have so much to gain from the cutting-edge joint research and innovation programmes we are driving, as well as the backing we attract from commercial investors and research companies.
“I passionately believe that working together in this way will result in great jobs for local people, with the wider economic impact this has, and the reduction of inequalities in Leeds and across West Yorkshire.”
Dr Linda Pollard
Professor Simone Buitendijk, Vice-Chancellor of the University, said: “It is fantastic news that three of our colleagues have been recognised in the Queen’s Birthday Honours List.
"What unites them is their strong belief in advancing research and knowledge to benefit the public and the wider community.
“The honours represent a considerable personal achievement to each of the recipients but they are also a reflection on the strengths and ethos of the University and the vision for the city of Leeds to be seen as a place of research and teaching excellence.”