This study investigated the effects of L-glutamine and L-glutamate (Gln/Glu) on growth performance and intestinal health of nursery pigs fed low digestible lysine diets. Piglets (n = 150; 21-day-old; 5.6 ± 0.55 kg initial BW) were distributed in a randomized block design, with three treatments and ten replicates. Experimental diets were fed from 21 to 33 and 33 to 47 d of age. The treatments consisted of control, standard lysine level; low-lys, 90% of the lysine level of the control diets; low-lys + Gln/Glu, low-lys diets supplemented with 1.2% and 0.8% of Gln/Glu (AminoGut, Ajinomoto) per phase. Alanine, inert and starch were used to make treatments isoproteic and isocaloric. Data were analyzed with SAS 9.4 PROC GLM. From 21 to 33 d, pigs fed control or low-lys + Gln/Glu diets had improved ADG, G:F, and 33-d BW compared with those fed low-lys diets (P < 0.05). From 21 to 47 d, pigs fed control or low-lys + Gln/Glu diets had improved ADG and 47-d BW compared with those fed low-lys diets (P < 0.05). The supplementation of Gln/Glu in the diets improved G:F compared with those fed low-lys (P < 0.05). Pigs fed low-lys + Gln/Glu had greater duodenum villus height compared with those fed low-lys (P < 0.05), and pigs fed the control diet had intermediate results. Pigs fed control diets had increased presence of goblet cells in duodenum compared with those fed low-lys (P < 0.05), and pigs fed the low-lys + Gln/Glu diet had intermediate results. Pigs fed low-lys + Gln/Glu diets had increased presence of goblet cells in jejunum compared with the other treatments (P < 0.05). The diets did not influence Peyer’s patches count (P > 0.05).