$Y$ combinator is defined as:
$$\text{Y}\ :=\ \lambda f. (\lambda x.f(xx))\ (\lambda x.f(xx))$$
To convert it to SKI-combinators, first apply lambda lifting:
$$ \lambda x.f(xx) = (\lambda f.\lambda x.f(xx))\ f\ =:\ H f$$
Writing in combinators notation,
$$ H f x = f (x x) $$
$$ Y f = H f (H f) = f(Hf(Hf)) $$
Now we can convert the $Y$ and $H$ definitions by matching right-hand sides of the combinator equations
$\qquad\begin{align}
I a &= a
\\ K a b &= a
\\ S a b c &= a c (b c)
\\ S I I c &= I c (I c) = c c \end{align}$
then,
$\qquad\begin{align}
H f x &= f (x x) = K f x (SII x)
\\ &= S(Kf)(SII)x
\\ &= S(KS)Kf(K(SII)f)x \\&= S(S(KS)K)(K(SII))fx \end{align}$
$\qquad\begin{align}
\ \ Y f &= Hf(Hf) = SII(Hf) \\&= K(SII)f(Hf) \\&= S(K(SII))H f \end{align}$
$\qquad\begin{align}
\ \ Y f &= Hf(Hf) = SHHf \\&= SSIHf \end{align}$
Substituting the $H$ definition gives us two possibilities, after $\eta$-contraction:
$$ Y = S(K(SII))(S(S(KS)K)(K(SII))) $$
$$ Y = SSI(S(S(KS)K)(K(SII))) $$
Applying the $S$ rule, the first definition can be further contracted to
$$ Y = SS(S(S(KS)K))(K(SII)) $$
which seems to be the shortest encoding of $Y$, also in terms of $SK$-letters only, since each $I$ counts as three (its explicit encoding shortly follows below).
Working with just $SKI$ combinators can fast become unwieldy. Adding more basic combinators helps:
$\quad\begin{align}
Babc &= a(bc) = Kac(bc) = S(Ka)bc \\
Cabc &= ac(b) = ac(Kbc) = Sa(Kb)c = S(K(Sa))Kbc \\
Wab &= abb = ab(SKab) = Sa(SKa)b = SS(SK)ab \\
&= abb = ab(Ib) = SaIb = CSIab = SS(KI)ab \\
Ub &= bb = Ibb = WIb = Ib(Ib) = SIIb \\
Ia &= a = Ka(Ka) = SKKa = SKSa \end{align}$
$U$ isn't usually included as a basic combinator, but it is arguably just as fundamental. Now we can have
$\quad\begin{align}
H f x &= f (xx) = f (Ux) = BfUx = CBUfx \\
H f x &= f (xx) = Bfxx = W(Bf)x = BWBfx \\
Y f &= H f (H f) = SHHf = SSIHf = WSHf \end{align}$
and thus the previous definitions were actually
$\quad\begin{align}
\ \ Y &= S(KU)(SB(KU)) = BU(CBU) \\
\ \ Y &= SSI(SB(KU))) = SSI(CBU) \\
\ \ Y &= SS(SB)(KU) \end{align}$
but now we've found yet other encodings,
$\quad\begin{align}
\ \ Y &= WS(CBU) \\
\ \ Y &= BU(BWB) = SSI(BWB) = WS(BWB) \end{align}$
There's also $Y = BU(CBU) = SB(CB)U = SSCBU $, but substituting the definitions in it leads to a very long $SK$-encoding, evidently.
To recap,
$\quad\begin{align}
\ \ Y &= S(K(SII))(S(S(KS)K)(K(SII))) \\
\ \ Y &= SSI(S(S(KS)K)(K(SII))) \\
\ \ Y &= SS(S(S(KS)K))(K(SII)) \end{align}$
These are 22(14), 18(12), 15(11) $SK(I)$-letters encodings. They are all different encodings for the same combinator definitions $Yf = Hf(Hf)$ and $Hfx=f(xx)$.
Using combinators instead of lambda-expressions makes it much easier to come up with a definition for a fixpoint combinator, in the first place:
$$ Yf = Hf(Hf) = f(Hf(Hf)) \ \ \models \ \ Hfx = f(xx) $$
$$ Y\text{′} f = HfH = f(HfH) \ \ \models \ \ Hfx = f(xfx) $$
$$ \Theta f = HHf = f(HHf) \ \ \models \ \ Hxf = f(xxf) $$
giving rise to
$$ Y = BU(CBU) = SS(S(S(KS)K))(K(SII)) $$
$$ Y\text{′} = WC(SB(C(WC))) = SSK(S(K(SS(S(SSK))))K) $$
$$ \Theta = U(B(SI)U) = SI(S(K(SI)))(SII) $$
(the $SK$-only encoding for $Y\text{′}$ is due to John Tromp, according to Wikipedia). These are 15(11), 12(12), 17(9) $SK(I)$-letters encodings.
It also holds that
$$ \Theta = WI( I( B(SI)(WI)) ) $$
$$ Y\text{′} = WC( C( B(SI)(WC)) ) $$
but this leads to a bit longer, 16(14)-long encoding
$$ Y\text{′} = SSK(S(K(S(S(K(SI))(SSK))))K) $$