Last year pupils' Higher exam results lifted Glasgow from the basement spot, closing the attainment gap between the city and the rest of Scotland.
For the first time since league tables were introduced, West Dunbartonshire took over the lowest spot.
But this year Glasgow is back in last place with just 7% of pupils passing five or more Highers in fifth year compared to 12% nationally.
For three or more Highers passed in fifth year, the city manages 16% of pupils, against a national average of 26%.
East Renfrewshire took the top spot in the league table with St Ninian's High School in Giffnock the best-performing state school in the country.
Mearns Castle High, in Newton Mearns, East Renfrewshire, came second.
Pupils in East Renfrewshire passing five or more Highers stands at 47% while the figure was 70% for three or more Highers.
For the council area as a whole the number was 33% for five Highers and 55% for three Highers.
Youngsters at the Glasgow Gaelic School achieved the best city council results in the city with 65% achieving three or more Highers, up from 36% last year.
However, education chiefs said the small number of pupils enrolled in the school meant that the comparison with other secondaries is skewed.
Donalda McComb, head teacher at Glasgow Gaelic School said: "I'm delighted for the young people and the staff at the school for all their hard work. We aim to build on this success."
Notre Dame School in the city's Hillhead also had excellent results, with 38% of pupils achieving three or more Highers and 18% at five or more.
Headteacher at Notre Dame, Philomena McFadden, said supported study, Saturday morning lessons, homework clubs and pupil support teams had helped boost attainment.
She said: "I am absolutely delighted for our young people, their parents and all the staff.
"Our success was a result of their combined efforts, as well as a number of strategies which were put in place to support our young people."
Education experts warn against using exam results alone as an indicator of how well schools are performing because they can be influenced by other factors depending on each institution's catchment area.
Despite the drop in Higher attainment this year, education bosses claimed standards are on the rise across Glasgow.
Director of education, Maureen McKenna, pointed to the levels of deprivation in the city, which makes comparisons with other local authorities unequal.
She said schools have been tasked with helping pupils work harder towards their Standard Grade exams with the hope this will help boost Higher results.
Ms McKenna said: "Schools remain very focused on raising attainment and monitor young people's progress carefully.
"Also, schools have very effectively built on the strong performance at Standard Grade in 2010. Attainment is increasing and we have closed the gap between the national position in 2010 and the position in 2011."
Results for Standard Grade exams were up for Glasgow pupils achieving five or more awards at General level and remained stable for those achieving five or more at Credit level.
Jean McFadden, Executive Member for Education, added: "Passes in Standard Grades at all levels are increasing and we should see this reflected in the Higher results next year.
"The extra teachers employed in our secondary schools and more than £500,000 additional investment will have an impact."
East Renfrewshire Council's education convener, Alan Lafferty, praised the council's education department .
He said: "The performance of our schools right across the board is cause for celebration.
"They have delivered superb results.
"These results show that with dedication, hard work and partnership between schools, pupils, parents, our education service and the wider community our young people will rise to the challenge."
Only Jordanhill School in Glasgow's West End, which is not council-run and has a unique direct funding deal, could boast similar results to East Renfrewshire.
It was third in Scotland, with five or more Highers (45%) and three or more Highers at 77%.
At the other end of the scale, the city's Castlemilk, Govan, Lochend Community, St Margaret Mary's and St Paul's high schools all had no pupils earning five or more Highers.