Background: While cigarette and passive smoking have been identified as modifiable risk factors for multiple sclerosis (MS), there is no report regarding Waterpipe smoking–MS association. Objective: We examined the association of Waterpipe, tobacco, and passive smoking with MS. Methods: Population-based incident case–control study in Iran with 547 incident cases and 1057 general population controls (7 August 2013–17 February 2015). Logistic regression model was used. Multiplicative along with additive interaction was assessed using product term and Synergy Index (SI), respectively, and the population attributable fractions (PAFs) were calculated. Results: Having ever smoked Waterpipe, tobacco, or being exposed to passive smoking were all significantly associated with MS (odds ratio (OR) = 1.77 (1.36–2.31), OR = 1.69 (1.24–2.31), and OR = 1.85 (1.48–2.32), respectively). Clear dose–response associations were observed with the duration exposed (p < 0.001 for all three) and the amount smoked (p < 0.001 for Waterpipe and tobacco). Those who had all three types of smoking had an odds that was 4.1 times higher than those without any type. The three types of smoking jointly contributed to 30.9% of the MS incidence. Conclusion: We identified Waterpipe smoking as a novel risk factor for MS. Given the global increase in Waterpipe smoking, especially among young adults, this finding reinforces the need for public health interventional and educational programs to combat this global increase.