This study examined whether teachers' professional development of their relational competence with students with attention deficit hyperactivity disorder (ADHD) and/or autism spectrum disorder (ASD) modifies teachers' and students' perceptions of their teacher-student relationships (TSR). Participants comprised teachers (n = 33) and students (n = 232) from two elementary schools: one intervention school (InS) and one control school (CoS). InS teachers reported significant TSR improvements, regardless of student group or gender (p = 0.03). Among InS students, significant results were driven by female neurodiverse (ND) students and neurotypical (NT) male students (p = 0.03). Nevertheless, positive effects were solely observed among ND female students, while NT male students, conversely, reported decreased TSR during follow-up tests. No significant effects were found at the CoS irrespective of teacher or student ratings. The findings suggest that enhancing teachers' understanding of relational competence concerning ND students will not only improve their own perceptions of their TSR but also those of ND female students. Nonetheless, directing teachers' focus towards one student group (ND students) risks diminishing teachers' attention towards other student groups, potentially explaining the poorer follow-up results among NT boys. The finding warrants further investigation, as it indicates a challenge for teachers to establish sufficient relational engagement with all students.