Background: Preventing smoking uptake among young people is a public health priority. Further education (FE) settings provide access to the majority of 16- to 18-year-olds, but few evaluations of smoking prevention interventions have been reported in this context to date. Objectives: To evaluate the feasibility and acceptability of implementing and trialling a new multilevel smoking prevention intervention in FE settings. Design: Pilot cluster randomised controlled trial and process evaluation. Setting: Six UK FE institutions. Participants: FE students aged 16–18 years. Intervention: ‘The Filter FE’ intervention. Staff working on Action on Smoking and Health Wales’ ‘The Filter’ youth project applied existing staff training, social media and youth work resources in three intervention settings, compared with three control sites with usual practice. The intervention aimed to prevent smoking uptake by restricting the sale of tobacco to under-18s in local shops, implementing tobacco-free campus policies, training FE staff to deliver smoke-free messages, publicising The Filter youth project’s online advice and support services, and providing educational youth work activities. Main outcome measures: (1) The primary outcome assessed was the feasibility and acceptability of delivering and trialling the intervention. (2) Qualitative process data were analysed to explore student, staff and intervention team experiences of implementing and trialling the intervention. (3) Primary, secondary and intermediate (process) outcomes and economic evaluation methods were piloted. Data sources: New students at participating FE settings were surveyed in September 2014 and followed up in September 2015. Qualitative process data were collected via interviews with FE college managers (n = 5) and the intervention team (n = 6); focus groups with students (n = 11) and staff (n = 5); and observations of intervention settings. Other data sources were semistructured observations of intervention delivery, intervention team records, ‘mystery shopper’ audits of local shops and college policy documents. Results: The intervention was not delivered as planned at any of the three intervention settings, with no implementation of some community- and college-level components, and low fidelity of the social media component across sites. Staff training reached 28 staff and youth work activities were attended by 190 students across the three sites (< 10% of all eligible staff and students), with low levels of acceptability reported. Implementation was limited by various factors, such as uncertainty about the value of smoking prevention activities in FE colleges, intervention management weaknesses and high turnover of intervention staff. It was feasible to recruit, randomise and retain FE settings. Prevalence of weekly smoking at baseline was 20.6% and was 17.2% at follow-up, with low levels of missing data for all pilot outcomes. Limitations: Only 17% of eligible students participated in baseline and follow-up surveys; the representativeness of student and staff focus groups is uncertain. Conclusions: In this study, FE settings were not a supportive environment for smoking prevention activities because of their non-interventionist institutional cultures promoting personal responsibility. Weaknesses in intervention management and staff turnover also limited implementation. Managers accept randomisation but methodological work is required to improve student recruitment and retention rates if trials are to be conducted in FE settings. Trial registration: Current Controlled Trials ISRCTN19563136.