It found that across all decile groupings achievement of at least NCEA Level 2 upon leaving school was higher at boys' schools.
Maori and Pasifika school leavers from boys' schools were more likely than their counterparts in co-ed schools to gain qualifications.
NZCER chief researcher Cathy Wylie said some of the boys' schools looked at were achieving fantastic results for their students, with many greatly improving their results in recent years.
However, she cautioned against parents taking the results as evidence that single-sex schools were better.
Other factors at play included school size, and boys' schools including more integrated schools, which could attract parents more ready to provide financial and other support.
The report also noted that boys at some co-ed schools performed as well or better than their counterparts at boys' schools.
A key task of the report was to identify what high-performing boys' schools were doing right, so that other schools could learn from them.
For example, schools set-up mentoring relationships between older boys and recent arrivals, with some stressing a concept of legacy - asking boys what they wanted to be known for or have achieved come the end of year.
"For me, it's not saying one kind of school is better than another," Ms Wylie told the Herald.
"But quite a few of the boys' schools have used a lot of the knowledge we have about how to make for really good learning, they've put it into practice and you are seeing the results."
Are boys' schools better?
# New research finds boys who attend boys' secondary schools are more likely to leave with qualifications than their male counterparts at co-educational schools.
# Researchers have identified what the top-performing boys' schools are doing well.
# They say what is going on inside a school should be of more concern to parents than whether it is single-sex or co-educational.
