Mr Lee founded the company in 1999, and oversaw its growth into the UK’s largest online pharmacy.
His departure is part of a “small handful of changes made to the business and its workforce” of more than 300 employees, the company said.
Chief executive Mark Livingstone said: “It’s been fantastic to have worked with Dan over the last three years. Having pioneered the distant dispensing sector over the last 20 years, we are all extremely grateful to him and wish him every success in the future”.
Mr Lee told C+D: “Having pioneered digital pharmacy 20 years ago, the timing couldn't be better to pursue new opportunities, as the market matures and new business models emerge.”
In 2016, Mr Lee received a warning from the General Pharmaceutical Council (GPhC) after a scandal that saw Pharmacy2U fined £130,000 for allowing patient data to be sold to a third party marketing company.
Mr Lee told a GPhC hearing at the time that the sale of data – which ended up in the hands of an Australian lottery company – was a “mistake” and he had not been directly involved.