The raids form part of a nationwide operation to prevent unapproved medical devices being sold online. Many appear on eBay and are priced below market value.
Dr Nicola Lennard, deputy clinical director at the MHRA, said: "Inaccurate readings from cheap, fake thermometers could result in a delay to a child getting the medical treatment they need and it is vital that people do not buy or use cheap, unapproved medical devices.
"The MHRA is working with internet sites to ensure that fake medical devices are not sold to people and we urge the public to report faulty medical devices."
The fake thermometers have no recognised brand name and often lack the requisite safety markings, warnings and instructions for use.
They can be identified by missing details such as an absence of a batch identification number, no CE mark to prove the item meets European standards and no four-digit identification number to show it has been through the appropriate safety assessment. Many are also sold without an instruction leaflet.