This study determined the perception and challenges encountered by college teachers in teaching mathematics online. The researcher utilized a quantitative design. The locale study was at Cagayan State University on all its eight campuses: Andrews, Aparri, Carig, Gonzaga, Lallo, Lasam, Piat, and Sanchez Mira for the school year 2021-2022. Descriptive statistics were utilized in the treatment of data gathered. The analysis of variance or independent samples t-test was used to determine the difference between the teacher’s profile and their perception of online teaching. Based on the findings, the group of respondents was female-dominated and in middle adulthood. The result manifested that teacher–respondents had been into continuous professional development through enrollment in advanced studies. In addition, the faculty members in the locale of the study are composed of young professional teachers. Results revealed that teachers’ level of perception toward online teaching in Mathematics is high. Also, the challenges teachers encounter in teaching mathematics online are to a great extent. Moreover, there is a significant difference between participants’ mean level of perception towards online learning when grouped according to the length of years in teaching mathematics. On the other hand, no significant difference was found in other variables such as age, sex, highest educational attainment, and their mean level of perception towards online learning. Also, there is a significant difference between the mean level of challenges encountered by the participants in online learning when grouped according to age. In conclusion, there is a high level of teachers’ perception toward online teaching and a great extent of challenges teachers encounter in teaching mathematics online. Also, older teachers found it difficult to develop interesting content, describe, and provide feedback using e-learning systems. Moreover, there is a need for the university to conduct training on online teaching strategies for mathematics teachers.