An "important milestone" was reached with eight months still to go before the 30 June 2021, deadline, the UK Home Office said in a statement.
According to the statement, nearly 3.8 million applicants have already been granted permission to remain in the UK once Brexit is fully delivered.
"European citizens are an integral part of our society, culture and community which is why I'm really proud we've already surpassed four million applications to the hugely successful EU Settlement Scheme", Minister for Future Borders and Immigration Kevin Foster was quoted as saying.
The latest statistics also show that of the more than 4 million applications across the UK, there have been nearly 3.7 million from England, 204,700 from Scotland, 67,200 from Wales and 66,300 from Northern Ireland up to the end of September 2020.
The Home Office also said that a dedicated team of more than 1,500 people are working seven days a week to help EU citizens with their applications to the settlement scheme.
"A wide range of support is available online and over the telephone, if you need it and we are funding 72 organisations across the UK to help the more vulnerable in society", Foster added.
Activist group The3million has raised concerns due to applicants who are granted the right to remain in the UK not being issued a physical document proving their status.
The so-called EU Settlement Scheme has been fully open since 30 March 2019, and at its height, Home Office caseworkers were regularly processing up to 20,000 applications a day.
The UK left the European Union on 31 January, but as part of the Withdrawal Agreement, both parties agreed on an 11-month transition period to negotiate their future relations concerning trade and other issues.