The tiny tribute, which reads "Happy 90th Birthday Your Majesty", was inscribed by staff at the University of Nottingham's new Â£12m nanoscale research centre.
Hairs used in the experiment - roughly a tenth of a millimetre wide - are from corgis related to the royal pets.
The team previously drew a tiny Queen's face to mark her Diamond Jubilee.
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Christopher Parmenter, from the university's School of Pharmacy, explained how the message was written using nanotechnology.
The scientists used an electron microscope, which projected a beam of ions onto the hair's surface, removing the top layer to allow the message to be etched.
"It's a truly magical process to observe that message just all of a sudden pop out, and we're hoping to send it to the Queen herself," Mr Parmenter said.
Dr Michael Fay said a number of key scientific advancements are being developed through nanoscale and microscale analysis.
"It could be better computers or treatments for cancer. They all come from understanding things down from the very small scales," he said.
The university currently hold a Guinness world record for creating the smallest periodic table.
Scientists said more than a million copies of the table could fit on a single slip of note paper.
A team of university scientists have etched a microscopic birthday message for the Queen - on the hair of a corgi.