This study is aimed at exploring the effects on Science Inquiry Ability, Scientific Attitude and Science Achievement of the Elementary School Students according to the Input time of Web-Based Instruction Programs. As the object of the study, seventy-two students were selected from three classes in the fifth grade of Y Elementary School located in the city of T, Gyungsangnam-do. They were classified into the three groups such as Group A (Class 1), Group B (Class 2) and Group C (Class 3). The author threw web-based instruction programs into the begining of a unit, during a unit, the end of a unit to each group, and explored the effects. The results of this study were as follows: First, for the learning effect of science inquiry ability, it was indicated that there was the highest effect in the case of throwing web-based instruction programs into during a unit, but the effect reduced a little in the case of throwing them into the end of a unit. Secondly, the scientific attitudes tended to be reduced in the case of throwing them into during a unit, but there did not occur statistically significant improvement. Thirdly, the degree of improvement of the science achievement tended to be highest in the case of throwing them into the end of a unit. Such findings indicated that the time of throwing in web-based instruction programs affected science inquiry ability, scientific attitude and science achievement of elementary school students. Thus, it will be said that teachers need to teach their students with the class strategies of considering various scientific elements revealed at the time of throwing in web-based instruction programs.