Li Yin graduated with honours from the University of Edinburgh, Scotland and completed her foundation programme at the South East of Scotland Deanery. Following that, she returned to her alma mater for her PhD studies and secured funding from Cancer Research UK for a Clinical Research Training Fellowship. Under the mentorship of Professor Malcolm Dunlop and Dr Susan Farrington of the Colorectal Cancer Genetics group, she worked on post-GWAS functional characterization of colorectal cancer susceptibility loci.

After receiving her doctorate degree, she went on to pursue her residency training in anatomical pathology at the National University Hospital of Singapore and obtained fellowship from the Royal College of Pathologists of Australasia.