The incidence of tick-borne encephalitis (TBE) has increased in the Nordic countries in recent years, highlighting the importance of detecting and sequencing tick-borne encephalitis virus (TBEV). The aim of this project was to detect and partially sequence TBEV in tick samples collected in Åland, Finland, and in human samples collected in Örebro, Sweden, thereby contributing to the monitoring of TBEV subtypes and strains circulating in these regions. Nested PCR was performed, amplifying five different regions of the genome. PCR products were analyzed by gel electrophoresis, and amplicons of the expected size were purified and subjected to Sanger sequencing. Sequence alignment and chromatogram correction were performed using SnapGene Software, and BLAST analyzes were conducted to identify the closest matching sequences. TBEV was confirmed in eight of the 31 tick samples by sequencing of the 5′NCR, two for the NS4B/NS5 region, and two for the 5′NCR-prM region. Sequence analysis revealed high similarity to the TBEV strain K23, as well as to sequences originating from Ixodes scapularis and Homo sapiens. In contrast, none of the human serum or cerebrospinal fluid samples could be confirmed as TBEV. Because several tick-derived sequences showed complete identity to the K23 vaccine strain, which had been used as a positive control during real-time qPCR analyses, contamination was considered as a possible explanation for these findings.