One of the aims for compulsory education is to diminish or alleviate differences in children’s skills existing prior to school entry. However, a growing gender gap in reading development has increasingly been documented. Regrettably, there is scant evidence on whether differences between genders (favouring girls) have their roots in pre-reading skills or whether determining mechanisms are related to factors to do with schooling. We examined the extent to which pre-reading skills assessed in Kindergarten (age 6) predict reading comprehension in Grade 9 (age 15) and, whether the gender difference in reading comprehension can be explained by gender differences in the Kindergarten pre-reading skills. A sample of 1010 Finnish children were assessed on letter knowledge, phonological awareness, rapid naming, vocabulary, and listening comprehension in Kindergarten and on reading comprehension using PISA Reading tasks in Grade 9. Path models showed that gender as well as Kindergarten pre-reading skills except for phonological awareness were significant predictors of reading comprehension in Grade 9 accounting for 28% of the variance. There were gender differences in most of the measures, but the prediction model estimates were similar for boys and girls except that for boys, letter knowledge was a somewhat stronger predictor of reading comprehension than for girls. The gender effect on reading comprehension was only partially mediated via pre-reading skills. The findings suggest that Kindergarten pre-reading skills are powerful predictors of reading comprehension in Grade 9, but the gender difference found in PISA Reading in Finland does not appear to be pronounced in Kindergarten but rather emerges during the school years.