Circlator is a novel tool designed to automate the circularization of genome assemblies using long sequencing reads. The tool addresses the challenge of completing and circularizing bacterial and small eukaryotic genomes, which are now possible due to emerging technologies capable of producing reads tens of kilobases long. Circlator correctly circularized 26 out of 27 circularizable sequences, including 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of *Plasmodium falciparum*, and a human mitochondrion. The tool uses local assemblies of corrected long reads at contig ends to circularize contigs, avoiding the need for manual intervention and allowing circularization even when overlaps are absent. Evaluations using various datasets, including bacterial PacBio data, *P. falciparum* apicoplast and mitochondrion genomes, and *Homo sapiens* mitochondrion, demonstrated that Circlator outperformed existing methods in terms of accuracy and efficiency. The tool is available at http://sanger-pathogens.github.io/circlator/.Circlator is a novel tool designed to automate the circularization of genome assemblies using long sequencing reads. The tool addresses the challenge of completing and circularizing bacterial and small eukaryotic genomes, which are now possible due to emerging technologies capable of producing reads tens of kilobases long. Circlator correctly circularized 26 out of 27 circularizable sequences, including 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of *Plasmodium falciparum*, and a human mitochondrion. The tool uses local assemblies of corrected long reads at contig ends to circularize contigs, avoiding the need for manual intervention and allowing circularization even when overlaps are absent. Evaluations using various datasets, including bacterial PacBio data, *P. falciparum* apicoplast and mitochondrion genomes, and *Homo sapiens* mitochondrion, demonstrated that Circlator outperformed existing methods in terms of accuracy and efficiency. The tool is available at http://sanger-pathogens.github.io/circlator/.