Home Office data published for the first time, shows around 40 people who applied to continue living in the area by the September 30 deadline had their application rejected.
The figures show that, since applications opened, 2,090 EU nationals in South Tyneside applied to continue living in the UK – with 1,980 getting a decision by the end of September.
Of them, 1,120 (57%) received settled status and 770 (39%) pre-settled.
People who have lived in the UK for five years, and meet the criteria, received settled status and can remain in the country indefinitely.
Those who have lived in the country for less time received pre-settled status, which allows them to remain for a further five years and later re-apply for settled status.
The highest number of applications came from citizens of Poland (460), Italy (310) and Romania (210).
Though the scheme officially closed on June 30, EU citizens can still apply.
Around 60 applications were submitted after the deadline in South Tyneside.
The Home Office said people with a pending application, are protected while the outcome of their application is unknown.
A spokeswoman said the EU Settlement Scheme has been an "overwhelming success", with 6.3 million applications received and 5.5 million people being granted permission to stay.
She added: “Individuals who have been refused can apply for an administrative review or appeal.
“We have published guidance on reasonable grounds for making a late application and take a flexible and pragmatic approach to considering them.”