This study examined the relationship between middle school students’ smart media competency and online learning outcomes in an inquiry-based mathematics and science environment. A total of 455 Korean students from grades 7–9 participated, and their smart media competency was measured using the Smart Media Literacy Quotient (SMLQ). Results showed that smart media literacy differed by gender, grade level, subject, and socio-economic status, with female, senior-grade, and non-minority students demonstrating higher competency. Higher smart media literacy was also associated with better inquiry-task performance, while low achievers and students who dropped out exhibited significantly lower smart media literacy and more negative beliefs toward smart media.