Background: Clostridium perfringens causes intestinal injury through overgrowth and secretion of multiple toxins, leading to diarrhea and necrotic enteritis in animals, such as pigs. Lactobacillus plantarum (L. plantarum) Lac16 has been reported to protect broilers against C. perfringens infection. This study aimed at investigating the protective effects of Lactobacillus plantarum Lac16 on C. perfringens infection-associated intestinal injury in intestinal porcine epithelial cell line (IPEC-J2). Results: The results showed that L. plantarum Lac16 significantly inhibit the growth and biofilm formation of C. perfringens (P < 0.001). In the co-culture system, L. plantarum Lac16 significantly suppressed colony forming units (CFU) of C. perfringens (P < 0.05), which was accompanied by a decrease in pH levels (P < 0.01). Moreover, L. plantarum Lac16 significantly elevated the mRNA expression levels of host defense peptides (HDPs) in IPEC-J2 cells (P < 0.05), decreased C. perfringens-induced cellular cytotoxicity (P < 0.01) and adhesion to cells (P < 0.05). At the same time, L. plantarum Lac16 significantly attenuated C. perfringens-induced damage to intestinal barrier integrity and the decrease in claudin-1 (P < 0.01) as well as zona occludens 1 (ZO-1) expressions. Preincubation with L. plantarum Lac16 significantly suppressed mRNA expression levels of pattern recognition receptors (PRRs) (Toll-like receptor (TLR) 1, TLR2, nucleotide-binding oligomerization domain (NOD) 1) in C. perfringens-challenged IPEC-J2 cells (P < 0.01). C. perfringens significantly elevated the phosphorylation of p38 mitogen-activated protein kinase (MAPK), JNK, and p65 nuclear factor-κB (NF-κB) (P < 0.05) while L. plantarum Lac16 pre-incubation effectively inhibited phosphorylation of p65 (P < 0.001). Furthermore, L. plantarum Lac16 significantly suppressed C. perfringens induced gene expressions of proinflammatory cytokines (interleukin (IL)-1β, IL-6, IL-8, tumor necrosis factor-α (TNF-α)) (P < 0.05). Conclusions: Collectively, probiotic L. plantarum Lac16 exerts protective effects against C. perfringens infection-associated intestinal injury in IPEC-J2 cells.