Glass ionomer fissure sealant (GIS) and fluoride varnish (NaFV) are two preventive interventions applicable to pre-school children. However, their application effects on young children's behaviour are understudied. The study compared the effects of GIS and NaFV applications on dental anxiety (DA), cooperativeness and pain level in pre-school children when applied to primary second molars in outreach settings. Four hundred and thirteen children were recruited for the study, out of which 228 were allocated to NaFV group whilstand 185 allocated to the GIS group. One calibrated examiner screened and randomly allocated the children into either group. Another calibrated examiner recorded the children's DA level and cooperativeness with Frankl Behaviour Rating Scale (FBRS) and Venham Behaviour Rating Scale (VBRS) throughout the treatment period. Subjects self-reported their pain levels using Wong-Baker Faces Scale (WBFS). Significant difference in postoperative anxiety was found using VBRS, with children in NaFV group having more positive scores post-treatment (p = 0.016). Only the type of preventive interventions significantly affected postoperative DA and patient cooperation (p = 0.032), whereas no other clinical findings and socio-demographic factors significantly influenced the children's behaviour postoperatively. NaFV application is associated with less DA and more cooperative behaviour in pre-school children compared to GIS application although similar pain levels were recorded.