Social media has become something that is important to enhance social networking and sharing of information through the website. Social media have not only changed social networking, they provide a valuable tool for social organization, activism, political, healthcare and even academic relations in the university. The researchers conducted present study with objectives to a). examine the academic use of social media by universities, b). measure the popularity and visibility of social media owned by universities. This study was delimited to the universities in Indonesia. The population of the study consisted both on public and private universities. The sample size comprised totally of 264 universities that their ranks included both in Webometrics and 4ICU in July 2012 edition. The social media which was examined included Facebook, Twitter, Flicker, LinkedIn, Youtube, Wikipeda, Blogs, social network community owned by the university and Open Course Ware. This study used an approach for data collection and measurement: by using Alexa and Majestic SEO. Data analysis using the Pearson Chi-square for social media ownership that using data ordinal and independent t test for examining effects of social media on website popularity. The study revealed that majority of the social media users used Facebook, then followed by Twitter. There are also most significant differences for result of popularity by Alexa Rank and visibility by Majestic SEO in universities whether used social media or no.