Palicourea boqueronensis is characterized by its glabrous vegetative and reproductive structures; relatively small, elliptic leaf blades, 2-6 × 1-2 cm, that are chartaceous and shiny on one or both surfaces; stipules united around the stem into a truncate sheath with two narrowly triangular lobes on each side; pedunculate, rather short, spiciform to racemiform inflorescences with the flower-bearing portion 1-2 cm long and the flowers subsessile in heads or short cymes at four to six nodes; dentate calyx limbs 0.8-1 mm long; slenderly funnelform, white, 5-lobed corollas with the tube ca. 4 mm long and the lobes ca. 2 mm with an abaxial conical appendage ca. 0.3 mm long; weakly didymous fruits 3.5--4 mm in diameter; and pyrenes abaxially with four to five broad angles. The leaf blades appear to be rather fleshy in life. These have the secondary veins thinly impressed on the upper surface, and the secondary veins and sometimes some of the tertiary venation raised on the lower surface but the remaining venation not visible here. The stipule lobes are 1-2 mm long, and adaxially bear one or two glandular appendages 1-2 mm long; on young stipules, these glandular appendages extend beyond the tip of the lobes. Similar glandular appendages are borne adaxially on the sheath, and these appendages are all deciduous. The developing fruits first become orange, then purple-black at maturity. Specimens of this species characteristically dry with a yellowish brown color.
Palicourea boqueronensis is similar to Palicourea topoensis and Palicourea gonzaleziana.