A frictionless multi-factor authentication system and method (“FMFA system”) that facilitates verification of the identity of a website user, registrant or applicant. The FMFA system reduces or removes the burden on the user by eliminating the additional manual second step traditionally required by two-factor authentication methods, and replacing the second step with an automated authentication step based on the location of a mobile device that is associated with the user. The FMFA system may be utilized for authenticating users to access sensitive data on online accounts, applications and websites, download files, perform online transactions, store information through websites or data stores, or the like. The FMFA system allows registration information obtained from a previously-registered user to authenticate the user on subsequent visits or logins to the website.