Birmingham was one of three Midland authorities which failed to achieve the national standard in today's Key Stage 3 tables.
The results for 14-year-olds indicate progress made by pupils half-way through secondary education.
The Government believes failure to pass them puts youngsters at risk of underachieving at GCSEs.
How did your local school perform? Full league tables published in today's Birmingham Post
Wolverhampton and Sandwell also failed to make the average grade per pupil.
St Alban's CofE in Highgate, Birmingham, was named the worst in the country for KS3 results, failing even to get pupils to the level of competence expected of a primary school leaver.
While pupils at KS3 are expected to reach at least Level 5 - the equivalent of between 33 and 39 points - the 14-year-olds at St Alban's failed to achieve the 27 points 11-year-olds are expected to get to pass Level Four at Key Stage 2.
Regarding St Alban's, an LEA spokeswoman said: "They have recently had an Ofsted report which said they make good progress with the pupils.
"They are working with 50 per cent of children who have English as an additional language, a large number of newly-arrived pupils and a high turnover rate of 35 per cent at Key Stage 3."
One other Midland school - Rushall Community College in Walsall - also failed to get its pupils up to the level of competence in numeracy, literacy and science expected of an 11-year-old.
Education Walsall which runs the authority's LEA, said: "It is important to understand that these results relate to the now closed Manor Farm School rather than the new Rushall Community College."
A spokesman for the Department for Education and Skills said greater levels of support would be given to under-performing schools.
Education chiefs in Birmingham insisted the number of secondary schools failing to hit Government floor targets for Level 5 in English had decreased from 26 to 21 and from 23 to 14 in mathematics.
The city council's cabinet member for education Coun Les Lawrence (Con Northfield) said: "I am pleased we are continuing to make progress at Key Stage 3 where Birmingham is reflecting the national trends.
"I am delighted our performance is above the average for comparable urban cities and authorities."
But he admitted the results showed there was "more progress to be made at this level".