The effect of Web-based project learning on the science achievement and attitude of middle school students was investigated. Four classes of 9th grade at a coed middle school were divided into control and experimental groups. Web-based project instruction in which students utilized the Web to interactively carry out their projects was put into practice with the experimental group, while traditional instruction was employed with the control group. Pre- and post-test achievement and attitude scores were estimated through an analysis of covariance. Web-based project instruction was seen to be more effective in enhancing students’ science achievement and attitude than traditional instruction. In particular, the former instruction was most useful for improving higher level students’ achievement and attitude among the higher, middle, and lower level students of both groups, based on their academic achievement. The effect of Web-based project may result in eradicating negative cognition about gender difference.