Perineural invasion (
PNI
) is a common and characteristic feature of pancreatic ductal adenocarcinoma (
PDAC
) that is associated with poor prognosis, tumor recurrence, and generation of pain. However, the molecular alterations in cancer cells and nerves within
PNI
have not previously been comprehensively analyzed. Here, we describe our proteomic analysis of the molecular changes underlying neuro‐epithelial interactions in
PNI
using liquid chromatography–mass spectrometry (
LC
‐
MS
/
MS
) in microdissected
PNI
and non‐
PNI
cancer, as well as in invaded and noninvaded nerves from formalin‐fixed, paraffin‐embedded
PDAC
tissues. In addition, an
in vitro
model of
PNI
was developed using a co‐culture system comprising
PDAC
cell lines and
PC
12 cells as the neuronal element. The overall proteomic profiles of
PNI
and non‐
PNI
cancer appeared largely similar. In contrast, upon invasion by cancer cells, nerves demonstrated widespread plasticity with a pattern consistent with neuronal injury. The up‐regulation of
SCG
2 (secretogranin
II
) and neurosecretory protein
VGF
(nonacronymic) in invaded nerves in
PDAC
tissues was further validated using immunohistochemistry. The tested
PDAC
cell lines were found to be able to induce neuronal plasticity in
PC
12 cells in our
in vitro
established co‐culture model. Changes in expression levels of
VGF
, as well as of two additional proteins previously reported to be overexpressed in
PNI
, Nestin and Neuromodulin (
GAP
43), closely recapitulated our proteomic findings in
PDAC
tissues. Furthermore, induction of
VGF
, while not necessary for
PC
12 survival, mediated neurite extension induced by
PDAC
cell lines. In summary, here we report the proteomic alterations underlying
PNI
in
PDAC
and confirm that
PDAC
cells are able to induce neuronal plasticity. In addition, we describe a novel, simple, and easily adaptable co‐culture model for
in vitro
study of neuro‐epithelial interactions.