Let $$(M,J,g,\omega )$$
(
M
,
J
,
g
,
ω
)
be a 2n-dimensional almost Hermitian manifold. We extend the definition of the Bott–Chern Laplacian on $$(M,J,g,\omega )$$
(
M
,
J
,
g
,
ω
)
, proving that it is still elliptic. On a compact Kähler manifold, the kernels of the Dolbeault Laplacian and of the Bott–Chern Laplacian coincide. We show that such a property does not hold when $$(M,J,g,\omega )$$
(
M
,
J
,
g
,
ω
)
is a compact almost Kähler manifold, providing an explicit almost Kähler structure on the Kodaira–Thurston manifold. Furthermore, if $$(M,J,g,\omega )$$
(
M
,
J
,
g
,
ω
)
is a connected compact almost Hermitian 4-manifold, denoting by $$h^{1,1}_{BC}$$
h
BC
1
,
1
the dimension of the space of Bott–Chern harmonic (1, 1)-forms, we prove that either $$h^{1,1}_{BC}=b^-$$
h
BC
1
,
1
=
b
-
or $$h^{1,1}_{BC}=b^-+1$$
h
BC
1
,
1
=
b
-
+
1
. In particular, if g is almost Kähler, then $$h^{1,1}_{BC}=b^-+1$$
h
BC
1
,
1
=
b
-
+
1
, extending the result by Holt and Zhang (Harmonic forms on the Kodaira–Thurston manifold. arXiv:2001.10962, 2020) for the kernel of Dolbeault Laplacian. We also show that the dimensions of the spaces of Bott–Chern and Dolbeault harmonic (1, 1)-forms behave differently on almost complex 4-manifolds endowed with strictly locally conformally almost Kähler metrics. Finally, we relate some spaces of Bott-Chern harmonic forms to the Bott–Chern cohomology groups for almost complex manifolds, recently introduced in Coelho et al. (Maximally non-integrable almost complex structures: an h-principle and cohomological properties, arXiv:2105.12113, 2021).