At grades A to C, boys also outperformed girls in four subjects - including French and history, traditionally seen as areas dominated by girls.
But, despite signs that more able boys have closed the traditional gender gap, boys working at Standard grade General level are still lagging badly behind girls.
John McDonald, head of secondary schools at Glasgow City Council, outlined a range of strategies which the authority is asking teachers to employ to give a boost to boys' attainment. They include replacing the traditional "hands up" response to a question with a "thumbs up" gesture, or showing "coloured cards" to indicate their willingness to answer a question.
The responses are part of a suite of formative assessment techniques employed across schools, but also a recognition that boys don't want to appear the "teacher's pet" by seeming too keen to answer questions.
Mr McDonald said there was a move towards making learning less passive. Teachers should get boys more involved in class and do less "pen and paper stuff". For instance, when doing literature, they should try and involve boys in "role play".
Linked to the idea of promoting active learning is a proposal to reduce the listening element of lessons. Mr McDonald added that boys' concentration levels, particularly in English lessons, were poor. Following work with educational psychologists, the education department was advising teachers to break their lessons into shorter chunks - six or eight parts, instead of four.
A number of schools are inviting successful male role models, some of them former pupils, to speak to pupils. These include Glasgow millionaire businessman, Willie Haughey, who has made a number of visits to Holyrood Secondary.