Several studies have suggested health-related physical fitness (HRPF) as an important health marker and closely associated with overweight and obesity among children and adolescents. However, the relationship among HRPF and exercise habits, weight status, and fitness attitude remains unclear. Thus, this study aimed to explore the possible factors, including knowledge, attitude, self-efficacy and weight status, and how these factors could affect HRPF among junior high school students in Taiwan. A total of 1,628 valid participants from 7th, 8th and 9th grades were selected based on the stratified cluster random sampling throughout Taiwan. The fitness and Affecting Factors in Physical Fitness Survey data were collected in 2011. Descriptive statistics and binary logistic regression with backward elimination were adopted to examine the significance of data. The result showed that roughly one third (35.6%) of Taiwanese junior high school students reached 4 standards of HRPF, all items are above 25th percentile. The logistic regression model revealed that the strongest relationship with HRPF was weight status, and exercise habits were significantly influenced HRPF tests among male and female students. Furthermore, knowledge and self-efficacy showed significant positive effects on HRPF among female students, while only attitude had positive influence on HRPF among male students. Results also demonstrated the urban-rural difference on HRPF. To be specific, female students from North Taiwan showed better HRPF than female students from East, while male students from East obtained better HRPF than male students from North. In addition, male students in North also exhibited better HRPF compared to male students in South. Therefore, these findings suggest that government should contemplate the urban-rural difference on HRPF, schools should enforce physical education curriculum and interventions should focus on strengthening of fitness knowledge, attitude, and self-efficacy to develop regular exercise habit to decrease the obesity rate and to further improve HRPF among junior high school students in Taiwan.