Amoebic infection has post a health challenge on human health due to the lack of effective anti-amoebic drugs. Current anti-amoebic treatment regime relies on the repurposing of anti-fungal drugs such as fluconazole. However, current treatment regime is tedious and it has severe side effects. Also, the cyst stage of Acanthamoeba castellanii confers resistance to the drug treatment and causes relapse of amoebic infection. In this study, the hypothesis is that the fluconazole conjugated with L-cysteine and graphene oxide functionalized nanomaterial will be more potent than the original fluconazole compound. We perform various amoebic assays such as amoebicidal, amoebistatic, excystation, and encystation assays. In addition, we perform MTT assay to determine the viability of the human HaCaT cell upon treatment of various compounds. The results indicate that L-CYS-GO-FLZ has similar anti-amoebicidal and anti-encystation efficacy as fluconazole alone, but has stronger anti-amoebistatic and anti-excystation. Furthermore, L-CYS-GO-FLZ confers lower toxicity on human HaCaT cells compared to treatment by fluconazole. Hence, these results have supported the potential of this modified version of fluconazole (Graphene Oxide functionalized nanomaterial loaded with fluconazole) as an effective anti-amoebic agent to treat amoebic infections.