The main purpose of the study designed to analyze the challenges of online learning during the Covid -19 pandemic at the Higher education level in Pakistan. Using a simple random sampling technique, a sample of five hundred and fifty (550) Higher-level students were selected from the target population. The survey method was used for the purpose of data collection. Data were analyzed using descriptive statistics and a t-test for the gender-wise comparison of overall learning challenges of implementation of online learning using the SPSS. The results of the study included the need for face to face interaction, flipped classroom learning modalities, giving concise lectures with a shorter time period and increasing teacher-student interaction can be applied. Faculty needs training and students orientation in using online learning tools. Also provides technical experts in Universities. Creates an opportunity for students to use different technologies. Government should also develop national e-learning development centres in different cities of Pakistan.