Economic evaluation of tobacco control policies is common in high-income settings and mainly focuses on cigarette smoking. Evidence suggests that increasing the excise tax of tobacco products is a consistently effective tool for reducing tobacco use and is an efficient mechanism for increasing government revenues. However, less research has been conducted in low/middle-income countries where other tobacco forms are common. This paper presents insights from our work on the economics of waterpipe tobacco smoking conducted in the Eastern Mediterranean Region where waterpipe smoking originated and is highly prevalent. The specific areas related to economics of waterpipe smoking considered herein are: price elasticity, taxation, government revenue, expenditure and healthcare costs. This paper aims to provide practical guidance for researchers investigating the economics of waterpipe tobacco with potential implications for other novel tobacco products. We present lessons learnt across five thematic areas: data, demand, taxes, equity and health modelling. We also highlight knowledge gaps to be addressed in future research. Research implications include designing comprehensive assessment tools that investigate heterogeneity in waterpipe smoking patterns; accounting for cross-price elasticity of demand with other tobacco products; exploring the change in waterpipe tobacco smoking in response to a tax increase and analysing the equity impact of waterpipe tobacco control interventions.