This paper was conducted to examine the tools, strategies, and problems encountered in assessing student learning by pre-service teachers in science during their on-and-off campus clinical experience. A explanatory sequential mixed method design (Creswell, 2003) was used in this study. Three research-made instruments were used in this study: The Assessment Checklist for Student Teachers in Science, Focus Group Discussion (FGD) Questions, and the In-depth Interview Questions. There were 17 pre-service teachers participated from a teacher education institution. Findings of the study using Kruskal-Wallis One-way Analysis of Variance and Thematical Analysis using Phenomenological Reduction Method revealed the assessment tools used most frequently and least frequently, assessment strategies, and the problems encountered by pre-service teachers in science in assessing student learning. The findings also revealed that there was a significant difference in the use of rubric (p value=0.045) as the least frequently used assessment tool by pre-service teachers in science when grouped according to specialization.