The gender division was particularly noticeable in chemistry, where Year 8 boys' average score was 51 per cent, compared with the girls' 44 per cent. But as the able below right shows, Years 8 and 9 boys also pipped the girls in the other categories of the science test - physics, science in the environment, life science and earth science.
And the fact that the gender differences were not statistically significant, with the exception of Year 8 chemistry, is unlikely to spoil their sense of triumph. The Year 9 boys' average overall science mark was 562, compared with 542 for girls.
The gender divide was equally wide in Scotland (527:507), where the boys were significantly stronger in earth science and chemistry, but not in physics. Boys outscored girls in about three-quarters of the countries that took part in TIMSS, but in the top-ranking country, Singapore, the gender divide was minimal.
The difference in boys' and girls' maths scores was less pronounced, not only in England, but in the other countries surveyed. The average overall score for Year 9 English boys was only three ahead of the girls' (465:462). But the Year 8 English boys had a 17-point lead over the girls (484:467).
The authors of this week's report on England's performance in the tests acknowledge that the TIMSS scores differ from the results of the national curriculum key stage 3 assessments and suggest that this may be because of the type of questions used.
"There's evidence that the performance of girls is lower than that of boys on multiple-choice items," they say. "In TIMSS, about 80 per cent of questions were presented using a multiple-choice format, so this may have been a contributory factor to gender difference."