In this paper, a novel multi-inner analyte channel photonic crystal fiber (PCF) based surface plasmon resonance (SPR) sensor is proposed to analyse plasmodium falciparum parasitized human Red Blood Cells (RBCs) that leads to ague. The full vectorial finite element method (FV-FEM) is employed to investigate the key propagation characteristics of the proposed sensor, such as confinement losses, resonance conditions, sensitivities, resolutions, and their linearities. Metallic plasmonic layers of gold (Au) and silver (Ag) are utilised, with two distinct channel shapes being used (circular and square). There are two alternative scenarios reported to identify the phases of the plasmodium falciparum cycle (Ring, Trophozite, and Schizont) in RBCs. The maximum spectrum sensitivities for circular type analyte channels have been found to be 4500 nm/RIU and 4750 nm/RIU, with resolutions of 2.2x10-5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$2.2 \times 10<^>{-5}$$\end{document} RIU and 2.1x10-5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$2.1 \times 10<^>{-5}$$\end{document} RIU for y-polarized and x-polarized modes, respectively. The spectral sensitivities of the square-shaped analyte channel, on the other hand, are 5300 nm/RIU and 6250 nm/RIU, with resolutions of 2x10-5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$2 \times 10<^>{-5}$$\end{document} RIU and 1.6x10-5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1.6 \times 10<^>{-5}$$\end{document} RIU for y-polarized and x-polarized modes, respectively.