  We assess the impact of starspots on the evolution of late-type stars during
the pre-main sequence (pre-MS) using a modified stellar evolution code. We find
that heavily spotted models of mass 0.1-1.2\msun\ are inflated by up to $10$%
during the pre-MS, and up to 4% and 9% for fully- and partially-convective
stars at the zero-age MS, consistent with measurements from active eclipsing
binary systems. Spots similarly decrease stellar luminosity and $T_{\rm eff}$,
causing isochrone-derived masses to be under-estimated by up to a factor of $2
\times$, and ages to be under-estimated by a factor of 2-10$\times$, at 3 Myr.
Consequently, pre-MS clusters and their active stars are systematically older
and more massive than often reported. Cluster ages derived with the lithium
depletion boundary technique are erroneously young by $\sim 15$% and $10$% at
$30$ and $100$ Myr respectively, if 50% spotted stars are interpreted with
un-spotted models. Finally, lithium depletion is suppressed in spotted stars
with radiative cores, leading to a fixed-temperature lithium dispersion on the
MS if a range of spot properties are present on the pre-MS. Such dispersions
are large enough to explain Li abundance spreads seen in young open clusters,
and imply a range of radii at fixed mass and age during the pre-MS Li burning
epoch. By extension, this implies that mass, composition, and age do not
uniquely specify the HR diagram location of pre-MS stars.
