This research looks into the interplay between gender and student classroom participation and identities in higher education. Research literature demonstrates that variance is found in students‘ classroom participation. While some researchers attribute these differences to student gender, others are of the opinion that other contextual factors are responsible for students‘ differential classroom participation. Moreover, diverse research findings also confirm that universities are unfriendly places for females, where they are discriminated against in a host of ways. In the recent past, the number of universities in Khyber Pakhtunkhwa has substantially increased, as part of the government resolve for increasing access to higher education for all, regardless of religion, class, gender and race. Therefore, it was imperative to look into gender-based disparities that female students might face while endeavoring for getting higher education. Using a qualitative case study design, nine universities were purposively selected as sample for data collection, out of the total nineteen (19) public sector universities in Khyber Pakhtunkhwa. Representations to the all culturally diverse areas have been given while selecting the sample of the study. Data were gathered through semi structured interviews and observations from students and teachers of the given sample universities. Two (2) male and two (2) female students from a departments each in a university were interviewed, while two (2) male and two (2) female teachers from the selected departments were also interviewed. Similarly, two classrooms observations were done in the sampled departments of the universities. The results show that universities in Khyber Pakhtunkhwa present highly unfriendly environments for female students; male students disproportionately dominate classroom activities. The findings also show that teachers and students tend to endorse and practice culturally appropriate practices, which serve to disadvantage and deny female students equal learning opportunities. Moreover, female students were found to be facing discrimination from male students as well as from male faculty members. Female students are expected to adhere to the established cultural beliefs and expectations of Pakhtun patriarchal society; otherwise, they are considered and branded to be violating established social rules and codes. Cultural inequalities and discrimination are visible not only in classrooms but also outside classroom within universities. Female students also face harassment from both faculty members and male students to the level where even females themselves have internalized such behaviors as something normal and expected. So strong are the beliefs of male dominance in the minds of both male and female faculty members and students that females are considered inferior not only physically but also mentally and consequently their better than males‘ academic performance is branded as based on rote memorization.