A measurement of the elliptic flow ($v_2$) of prompt J/$\psi$ mesons in high-multiplicity pPb collisions is reported using data collected by the CMS experiment at a nucleon-nucleon center-of-mass energy $\sqrt{s_\mathrm{NN}} =$ 8.16 TeV. Prompt J/$\psi$ mesons decaying into two muons are reconstructed in the rapidity region in the nucleon-nucleon center-of-mass frame ($y_\mathrm{cm}$), corresponding to either $-$2.86 $\lt y_{\mathrm{cm}} <$ $-$1.86 or 0.94 $\lt y_{\mathrm{cm}} <$ 1.94. The average $v_2$ result from the two rapidity ranges is reported over the transverse momentum (p$_\mathrm{T}$) range from 0.2 to 10 GeV. Positive $v_2$ values are observed for the prompt J/$\psi$ meson, as extracted from long-range two-particle correlations with charged hadrons, for 2 $\lt p_{\mathrm{T}}<$ 8 GeV. The prompt J/$\psi$ results are compared with previous CMS measurements of elliptic flow for open charm mesons (D$^0$) and strange hadrons. From these measurements, constraints can be obtained on the collective dynamics of charm quarks produced in high-multiplicity events arising from small systems.