Hundreds of people climbed barbed wire fences which were not being guarded by police at the time.
The group which consisted mostly of young men entered Ceuta, while members of the Moroccan auxiliary force responsible for security on the ground withdrew as the young people passed.
The migrants were shouting "Long live Spain" as they entered the territory.
The mass crossing coincided with the arrival of more than 1,500 migrants swimming into the city over the past week, according to regional authorities.
Ceuta, together with Melilla – another Spanish autonomous city located in North Africa – represent the European Union’s only land borders with Africa.
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Both cities periodically experience surges in attempted crossings by migrants seeking to reach Europe.
Ceuta leader Juan Jesus Vivas urged Spain’s government to declare an emergency over the mass arrivals.
Some 752 migrants arrived in the UK on Wednesday after crossing the English Channel, the highest number on a single day so far this year.
The cumulative number of arrivals by small boats in 2026 now stands at 14,128, according to provisional figures from the Home Office.
This is down 42% on the equivalent point last year, when the total stood at 24,538.
It is also 15% below the figure at this stage in 2024, when the total was 16,712.
There were nine boats that arrived on Wednesday, which suggests an average of 84 people per boat.
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French police meanwhile have claimed they have been ordered not to stop migrants getting into boats bound for Britain.
After confronting officers on Hardelot beach, south of Boulogne, shadow home secretary Chris Philp was told that they had been told to let the migrants go.
While being filmed by his support team, Mr Philp was told by a French officer: “Our order is to let them go. We just have to say to them, ‘Don’t do that. It’s dangerous’.”
Mr Philp then asked: “So your orders are not to intervene,” to which the police officers replied: “We have to protect them.”
The Home Office wrote on X: “We are aware of posts circulating online that claim French law enforcement are failing to prevent small boat Channel crossings. UK-French cooperation has already stopped over 46,000 attempted crossings since the election.”
The latest day of large numbers crossing comes after new Prime Minister Andy Burnham hailed home secretary Shabana Mahmood’s attempts to clamp down.
Mr Burnham said on Wednesday: “The Home Secretary has brought forward a very vigorous plan in relation to this. And let’s remember of course the numbers can fluctuate.
"But overall boat crossings are down, down quite significantly year-on-year, so that does suggest that the plan is working.
"It’s about getting a grip on the entire situation, I raised this repeatedly through the Makerfield by-election. The public want to see control being exerted and while we’ve made progress there is more to do. And I recognise that completely."
However, Mr Philp said: “Shabana Mahmood has paid half a billion pounds of our money unconditionally, yet I saw gendarmes doing nothing today and they told me they had orders to take no physical action but just talk to the migrants.
“The only thing protecting our borders has been the rough weather in the Channel this year.
“Andy Burnham just said there was no problem. I saw with my own eyes today how out of touch he is.
“We need a proper plan to end these crossings – leave the ECHR which would enable us to deport all illegal immigrants within a week of arrival. Then they wouldn’t bother attempting the crossing.”
A Home Office spokesman said: “This Government is bearing down on small boat crossings, with removals of small boat migrants at record levels and asylum claims down by 12 per cent.
“The Home Secretary has signed a landmark new deal with France to boost enforcement action on beaches and put people smugglers behind bars. This builds on joint work that has stopped over 44,000 attempted crossings since the election.
“We have removed or deported almost 70,000 people who were here illegally, an increase of 41 per cent, and are going further to remove the incentives that draw illegal migrants to this country.”

Head of Investigations