One of the key ingredients in establishing the relation between input signal and output flux from a spectrometer is accurate determination of the spectrophotometric calibration. In the case of spectrometers onboard satellites, the accuracy of this part of the calibration pedigree is ultimately linked to the accuracy of the set of reference SEDs that the spectrophotometric calibration is built on. In this paper, we deal with the spectrophotometric calibration of infrared (IR) spectrometers onboard satellites in the 2 to 200 micron range. We aim at comparing the different reference SEDs used for the IR spectrophotometric calibration. The emphasis is on the reference SEDs of stellar standards with spectral type later than A0, with special focus on the theoretical model atmosphere spectra. Using the MARCS model atmosphere code, spectral reference SEDs were constructed for a set of IR stellar standards (A dwarfs, solar analogs, G9-M0 giants). A detailed error analysis was performed to estimate proper uncertainties on the predicted flux values. It is shown that the uncertainty on the predicted fluxes can be as high as 10%, but in case high-resolution observational optical or near-IR data are available, and IR excess can be excluded, the uncertainty on medium-resolution SEDs can be reduced to 1-2% in the near-IR, to ~3% in the mid-IR, and to ~5% in the far-IR. Moreover, it is argued that theoretical stellar atmosphere spectra are at the moment the best representations for the IR fluxes of cool stellar standards. When aiming at a determination of the spectrophotometric calibration of IR spectrometers better than 3%, effort should be put into constructing an appropriate set of stellar reference SEDs based on theoretical atmosphere spectra for some 15 standard stars with spectral types between A0V and M0III.