Harnessing RNA modifications in therapeutics has enabled breakthroughs in vaccines. Despite their importance in RNA stability and translation, the mechanisms of RNA modifications are poorly understood. N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotes and changes translational efficiency or reduces mRNA stability. We studied this modification in Plasmodium falciparum by disrupting the methyltransferase that makes m6A with a knock-sideways mislocalisation system. Recent developments in sequencing by Oxford Nanopore Technologies (ONT) have enabled the direct detection of m6A in RNA. We therefore disrupted the methyltransferase and used Nanopore direct RNA-sequencing to study differential methylation at multiple points during the P. falciparum lifecycle. We were able to detect differentially methylated transcripts after mislocalising the methyltransferase, confirming the utility of both the knock-sideways system and Nanopore RNA-sequencing in studying m6A in P. falciparum. We detected differentially expressed genes after disrupting the methyltransferase, and found removing m6A affected the 3’ end position of transcripts. Our work shows Nanopore RNA-seq can be used to detect m6A abundance and location in P. falciparum, proving it a valuable technique for studying the impact of RNA modifications on parasite biology.