The labeling technique for cells with over-thousand-nanometer near-infrared (OTN-NIR) fluorescent probes has attracted much attention for in vivo deep imaging for cell tracking and cancer metastasis, because of low scattering and absorption of OTN-NIR light by biological tissues. However, the intracellular behavior following the uptake of the single-walled carbon nanotubes (SWCNTs), an OTN-NIR fluorophore, remains unknown. The aim of this study is to investigate the time-dependent change in OTN-NIR fluorescence images of cultured murine cancer cells (Colon-26) following treatment with a recently developed OTN-NIR fluorescent probe, epoxide-type oxygen-doped SWCNTs (o-SWCNTs). The o-SWCNTs were synthesized by oxygenation of SWCNTs by ozone under ultraviolet irradiation and were dispersed in an aqueous solution of N-(carbonyl-methoxypolyethyleneglycol 2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine to prepare biocompatible o-SWCNTs (o-SWCNT-PEG). OTN-NIR fluorescent o-SWCNT-PEG showed an abnormal behavior following cellular uptake. OTN-NIR fluorescence was not observed in the cells after 24 h incubation with the o-SWCNT-PEG, but clearly increased with longer incubation time from three days after the treatment. This result was further confirmed by Raman microscopy, suggesting that OTN-NIR fluorescence intensity was associated with the cellular uptake of the o-SWCNT-PEG. These results suggest that the Colon-26 cells were successfully labeled by the o-SWCNT-PEG that emit OTN-NIR fluorescence. The o-SWCNT-PEG may aggregate in the cells over time, which could favor their internalization. This delayed concentration followed by a long retention of the o-SWCNT-PEG in cells will facilitate further biotechnological applications of the o-SWCNTs to in vivo deep OTN-NIR fluorescent imaging.