The thermal performance of a flat-plate solar collector (FPSC) using novel heat transfer fluids of aqueous colloidal dispersions of covalently functionalized multi-walled carbon nanotubes with β-Alanine (Ala-MWCNTs) has been studied. Multi-walled carbon nanotubes (MWCNTs) with outside diameters of (< 8 nm) and (20–30 nm) having specific surface areas (SSAs) of (500 m2/g) and (110 m2/g), respectively, were utilized. For each Ala-MWCNTs, waterbased nanofluids were synthesized using weight concentrations of 0.025%, 0.05%, 0.075%, and 0.1%. A MATLAB code was built and a test rig was designed and developed. Heat flux intensities of 600, 800, and 1000 W/m2; mass flow rates of 0.6, 1.0, and 1.4 kg/min; and inlet fluid temperatures of 30, 40, and 50°C were used to perform the test runs. Using water and nanofluids, the efficiency of the FPSC was found to increase with the increase in heat flux intensity and flow rate, and decrease with the increase in inlet fluid temperature. When applying nanofluids in the FPSC and as weight concentration and SSA increased, a reduction in the values of absorber plate temperature (AP) and tube wall temperature (TW) was observed down to 2.86% and 3.03%, respectively, while the FPSC’s efficiency increased up to 9.55% for 0.1-wt% Ala-MWCNTs < 8 nm at 1.4 kg/min, compared with water. Good agreement was obtained between the experimental values and MATLAB code predictions for AP, TW, and efficiency with maximum differences of 3.02%, 3.19%, and 3.26% for water, and 4.24%, 3.94%, and 12.64% for nanofluids, respectively. Consequently, the MATLAB code was judged suitable for modeling the nanofluid-based FPSC with suitable precision. It was proved that the positive effects of using nanofluids in the FPSC were higher their negative effects on pressure drop because all the calculated values of performance index (PI) were more than 1. As weight concentration and SSA increased, PI increased up to 1.095 for 0.1-wt% Ala-MWCNTs < 8 nm. Therefore, it was concluded that the nanofluids considered in this research can usefully be employed as working fluids in FPSCs for improved thermal performance, and the 0.1-wt% water-based Ala-MWCNTs < 8 nm nanofluid was fairly the distinguished one.