Berikut ini daftar jurnal yang dikelola oleh FMIPA Unesa:
| No | Nama Jurnal | Link | Akreditasi |
| 1 | Jurnal Riset Biologi dan Aplikasinya | https://journal.unesa.ac.id/index.php/risetbiologi | SINTA 2 |
| 2 | Jurnal Penelitian Fisika dan Aplikasinya (JPFA) | https://journal.unesa.ac.id/index.php/jpfa | SINTA 2 |
| 3 | LenteraBio : Berkala Ilmiah Biologi | https://journal.unesa.ac.id/index.php/lenterabio | SINTA 3 |
| 4 | Journal of Mathematical Pedagogy (JoMP) | https://journal.unesa.ac.id/index.php/JOMP | SINTA 3 |
| 5 | JPPS (Jurnal Penelitian Pendidikan Sains) | https://journal.unesa.ac.id/index.php/jpps | SINTA 3 |
| 6 | JCER (Journal of Chemistry Education Research) | https://journal.unesa.ac.id/index.php/jcer | SINTA 3 |
| 7 | Jurnal Riset Pendidikan dan Inovasi Pembelajaran Matematika (JRPIPM) | https://journal.unesa.ac.id/index.php/jrpipm | SINTA 3 |
| 8 | MATHEdunesa | https://ejournal.unesa.ac.id/index.php/mathedunesa | SINTA 3 |
| 9 | Jurnal Inovasi Pembelajaran Biologi | https://journal.unesa.ac.id/index.php/jipb | SINTA 4 |
| 10 | Jurnal Abdi | https://journal.unesa.ac.id/index.php/abdi | SINTA 4 |
| 11 | Jurnal Riset dan Aplikasi Matematika (JRAM) | https://journal.unesa.ac.id/index.php/jram | SINTA 4 |
| 12 | JPPIPA (Jurnal Penelitian Pendidikan IPA) | https://journal.unesa.ac.id/index.php/jppipa | SINTA 4 |
| 13 | UNESA Journal of Chemical Education | https://ejournal.unesa.ac.id/index.php/journal-of-chemical-education | SINTA 4 |
| 14 | UNESA Journal of Chemistry | https://ejournal.unesa.ac.id/index.php/unesa-journal-of-chemistry | SINTA 4 |
| 15 | Berkala Ilmiah Pendidikan Biologi (BioEdu) | https://ejournal.unesa.ac.id/index.php/bioedu | SINTA 4 |
| 16 | Inovasi Pendidikan Fisika | https://ejournal.unesa.ac.id/index.php/inovasi-pendidikan-fisika | SINTA 4 |
| 17 | MATHunesa | https://ejournal.unesa.ac.id/index.php/mathunesa | SINTA 4 |
| 18 | Inovasi Fisika Indonesia | https://ejournal.unesa.ac.id/index.php/inovasi-fisika-indonesia | SINTA 5 |
| 19 | Journal of Digitalization in Physics Education | https://journal.unesa.ac.id/index.php/dpe | Internasional Proyeksi Scopus |
| 20 | Journal of Ethnophysics | https://journal.unesa.ac.id/index.php/ethnophysics | Internasional Proyeksi Scopus |
| 21 | METAVERSE: Journal of Mathematic Teacher Professional Development Research | https://journal.unesa.ac.id/index.php/metaverse | Internasional Proyeksi Scopus |
| 22 | Jurnal Proyeksi Scopus Pak Fasih (Plant Nanomaterial Journal) | https://journal.unesa.ac.id/index.php/pnj | Internasional Proyeksi Scopus |
| 23 | Journal of the Indonesian Mathematics Education Society | https://journal.unesa.ac.id/index.php/jimes | – |
| 24 | Indonesian Chemistry and Application Journal | https://journal.unesa.ac.id/index.php/icaj | – |
| 25 | Jurnal Penelitian Pendidikan Matematika dan Sains | https://journal.unesa.ac.id/index.php/jppms | – |
| 26 | Sains & Matematika | https://journal.unesa.ac.id/index.php/sainsmatematika | – |
| 27 | Journal of Dedication in Community (JoDiC) | https://ejournal.unesa.ac.id/index.php/JoDiC | – |
| 28 | Pensa: E-Jurnal Pendidikan Sains | https://ejournal.unesa.ac.id/index.php/pensa | – |