Objectives We integrated an established participant-centred active vaccine safety surveillance system with a cloud-based pharmacy immunisation-recording program in order to measure adverse events following immunisation (AEFI) reported via the new surveillance system in pharmacies, compared with AEFI reported via an existing surveillance system in non-pharmacy sites (general practice and other clinics).Design A prospective cohort study.Participants and setting Individuals >10 years receiving influenza immunisations from 22 pharmacies and 90 non-pharmacy (general practice and other clinic) sites between March and October 2020 in Western Australia. Active vaccine safety surveillance was conducted using short message service and smartphone technology, via an opt-out system.Outcome measures Multivariable logistic regression was used to assess the primary outcome: differences in proportions of AEFI between participants immunised in pharmacies compared with non-pharmacy sites, adjusting for confounders of age, sex and influenza vaccine brand. A subgroup analysis of participants over 65 years was also performed.Results Of 101 440 participants (6992 from pharmacies; 94 448 from non-pharmacy sites), 77 498 (76.4%) responded; 96.1% (n=74 448) within 24 hours. Overall, 4.8% (n=247) pharmacy participants reported any AEFI, compared with 6% (n=4356) non-pharmacy participants (adjusted OR: 0.87; 95% CI: 0.76 to 0.99; p=0.039). Similar proportions of AEFIs were reported in pharmacy (5.8%; n=31) and non-pharmacy participants (6; n=1617) aged over 65 years (adjusted OR: 0.94; 95% CI: 0.65 to 1.35; p=0.725). The most common AEFIs in pharmacy were: pain (2%; n=104), tiredness (1.9%; n=95) and headache (1.7%; n=88); and in non-pharmacy sites: pain (2.3%; n=1660), tiredness (1.9%; n=1362) and swelling (1.5%; n=1121).Conclusions High and rapid response rates demonstrate good participant engagement with active surveillance in both pharmacy and non-pharmacy participants. Significantly fewer AEFIs reported after pharmacist immunisations compared with non-pharmacy immunisations, with no difference in older adults, may suggest different cohorts attend pharmacy versus non-pharmacy immunisers. The integrated pharmacy system is rapidly scalable across Australia with global potential.