Example using FreeBSD/amd64 and version 2.0.45. Change it according to the current version and desired architecture.

cd /tmp
fetch -m https://github.com/DNSCrypt/dnscrypt-proxy/releases/download/2.0.45/dnscrypt-proxy-freebsd_amd64-2.0.45.tar.gz
mkdir dnscrypt-proxy
tar -zxf dnscrypt-proxy-freebsd_amd64-2.0.45.tar.gz -C dnscrypt-proxy
mv dnscrypt-proxy/freebsd-amd64/dnscrypt-proxy /usr/local/bin/dnscrypt-proxy
chown root:wheel /usr/local/bin/dnscrypt-proxy
chmod +x /usr/local/bin/dnscrypt-proxy
mkdir -p /usr/local/etc/dnscrypt-proxy
cp dnscrypt-proxy/freebsd-amd64/example-dnscrypt-proxy.toml /usr/local/etc/dnscrypt-proxy/dnscrypt-proxy.toml

Edit the configuration /usr/local/etc/dnscrypt-proxy/dnscrypt-proxy.toml to suit your needs.
(I would suggest listen_addresses = ['127.0.0.1:5300'] to avoid conflicts with the regular pfSense DNS services, in addition to your own preferences regarding which servers to use, etc.)

Add this script to /usr/local/etc/rc.d/dnscrypt-proxy.sh and set its execution permissions with chmod +x /usr/local/etc/rc.d/dnscrypt-proxy.sh.

#!/bin/sh

# PROVIDE: dnscrypt_proxy
# REQUIRE: cleanvar SERVERS
# BEFORE: unbound

. /etc/rc.subr

name=dnscrypt_proxy
procname=/usr/local/bin/dnscrypt-proxy
pidfile=/var/run/${name}.pid
load_rc_config $name

command=/usr/sbin/daemon
command_args="-p ${pidfile} -f ${procname} -config /usr/local/etc/dnscrypt-proxy/dnscrypt-proxy.toml -syslog"

run_rc_command "$1"

dnscrypt-proxy should now start on boot (the .sh extension for the rc script triggers this without further integration), and it can also be started immediately with service dnscrypt-proxy.sh start (stop it with service dnscrypt-proxy.sh stop, etc.).

Log output appears in Status -> System Logs (System/General section).

To make proper use of dnscrypt-proxy, you'll likely want to configure the regular pfSense resolver to forward all queries there.

Assuming that Unbound is in use (referred to as DNS Resolver in the pfSense UI), this can be done by putting something like this in Services -> DNS Resolver -> Custom options (make sure that the IP and port numbers correspond to what you configured in /usr/local/etc/dnscrypt-proxy/dnscrypt-proxy.toml):

server:
  do-not-query-localhost: no

forward-zone:
  name: "."
  forward-addr: 127.0.0.1@5300

This forwarding configuration should now be reflected in Status -> DNS Resolver, where the performance of the local dnscrypt-proxy should be tracked alone.