The overall aim was to explore the relationship between recurrent pain and perceived problems with academic achievement among boys and girls in middle and late elementary school. This 3-year follow-up study was based on data from the Study of Health in School-aged Children from Umeå (Sweden) and included children attending grade 6 in years 2003 and 2006, and a follow-up 3 years later in grade 9 ( = 1524, participation rate 90%). Recurrent pain (head, stomach or back) at least doubled the odds of concurrent- and subsequent perceived problems with academic achievement. This applied for pain on a monthly and weekly basis, from single and multiple sites, and from each of the three studied pain sites. The odds increased with increasing pain frequency and number of pain sites. Problems with sleep, concentration or school absenteeism did not explain the association. .