  This paper summarizes the results of 13 years of timing observations of a
unique binary pulsar, PSR B1259$-$63, which has a massive B2e star companion.
The data span encompasses four complete orbits and includes the periastron
passages in 1990, 1994, 1997 and 2000. Changes in dispersion measure occurring
around the 1994, 1997 and 2000 periastrons are measured and accounted for in
the timing analysis. There is good evidence for a small glitch in the pulsar
period in 1997 August, not long after the 1997 periastron, and a significant
frequency second derivative indicating timing noise. We find that spin-orbit
coupling with secular changes in periastron longitude and projected semi-major
axis ($x$) cannot account for the observed period variations over the whole
data set. While fitting the data fairly well, changes in pulsar period
parameters at each periastron seem ruled out both by X-ray observations and by
the large apparent changes in pulsar frequency derivative. Essentially all of
the systematic period variations are accounted for by a model consisting of the
1997 August glitch and step changes in $x$ at each periastron. These changes
must be due to changes in the orbit inclination, but we can find no plausible
mechanism to account for them. It is possible that timing noise may mask the
actual changes in orbital parameters at each periastron, but the good fit to
the data of the $x$ step-change model suggests that short-term timing noise is
not significant.
